#
# $Id$
#
# -----------------------------------------------------------------------------------------------------							
#							
# This first section includes a set of "custom" QTs							
# which are commonly used but not defined elsewhere.							
#							
# Name	DataType	Scale	MAGE Subclass	isBackground	ConfidenceIndicator target QT	Channel	Description
>>>Tab2MAGE_FGEM[ebi.ac.uk]							
RMA	float	linear_scale	DerivedSignal				
Normalized	float	linear_scale	DerivedSignal				
Ratio	float	linear_scale	Ratio				
# -----------------------------------------------------------------------------------------------------							
#							
# Below is the curated list of QTs as prepared and maintained by the ArrayExpress curators.							
# This will be updated periodically with new releases of this package.							
#							
# NOTE TO SELF - this part of the file will be automatically generated by Datafiles::write_QTs.							
# Attempt no changes here unless you are sure they won't be overwritten.							
#							
# Name	DataType	Scale	MAGE Subclass	isBackground	ConfidenceIndicator target QT	Channel	Description
>>>AIDA[Raytest]							
Area [pixel]	float	linear_scale	SpecializedQuantitationType				Spot area in pixels.
Bkg SD Cy3	float	linear_scale	Error	1	Bkg [QL] Cy3	Cy3	Standard deviation of background channel Cy3.
Bkg SD Cy5	float	linear_scale	Error	1	Bkg [QL] Cy5	Cy5	Standard deviation of background channel Cy5.
Bkg [QL] Cy3	float	linear_scale	SpecializedQuantitationType	1		Cy3	Standard deviation of background channel Cy3.
Bkg [QL] Cy5	float	linear_scale	SpecializedQuantitationType	1		Cy5	Standard deviation of background channel Cy5.
Homogeneity [%] Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Percentage of dot deviation from homogenous intensity distribution channel Cy3.
Homogeneity [%] Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Percentage of dot deviation from homogenous intensity distribution channel Cy5.
Integral SD Cy3	float	linear_scale	Error		Integral [QL] Cy3	Cy3	Standard deviation of integrated raw intensity channel Cy3.
Integral SD Cy5	float	linear_scale	Error		Integral [QL] Cy5	Cy5	Standard deviation of integrated raw intensity channel Cy5.
Integral [QL] Cy3	float	linear_scale	MeasuredSignal			Cy3	Integrated raw intensity of spot Channel Cy3.
Integral [QL] Cy5	float	linear_scale	MeasuredSignal			Cy5	Integrated raw intensity of spot Channel Cy5.
Mean [QL] Cy3	float	linear_scale	MeasuredSignal			Cy3	Mean (Integral/Area) Channel Cy3.
Mean [QL] Cy5	float	linear_scale	MeasuredSignal			Cy5	Mean (Integral/Area) Channel Cy5.
Median [QL] Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Median of the raw pixel intensity of spot Channel Cy3.
Median [QL] Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Median of the raw pixel intensity of spot Channel Cy5.
Quality Cy3	boolean	unscaled	SpecializedQuantitationType			Cy3	Quality flag Channel Cy3.
Quality Cy5	boolean	unscaled	SpecializedQuantitationType			Cy5	Quality flag Channel Cy5.
Saturated [pixel] Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Measure of saturation pixels channel Cy3.
Saturated [pixel] Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Measure of saturation pixels channel Cy5.
>>>Affymetrix[Affymetrix]							
Probe Set Name	string_datatype	unscaled	SpecializedQuantitationType				The name of the probe set.
Detection	string_datatype	unscaled	PresentAbsent				A measurement indicating if the transcript was detected (Present), not detected (Absent) or marginally detected (Marginal). Can be one of "Absent", "Marginal", "Present" or "No Call".
Detection p-value	float	linear_scale	PValue		Detection		The p-value calculated for a given detection call.
Signal	float	linear_scale	DerivedSignal				A measure of the relative abundance of a transcript.
Number of Pairs	integer	linear_scale	SpecializedQuantitationType				The number of probe pairs in the probe set.
Number of Pairs Used	integer	linear_scale	SpecializedQuantitationType				The number of probe pairs in the probe set used in the Detection call.
CELIntensity	float	linear_scale	MeasuredSignal				The intensity value of the probe. Represents the 75th percentile among the DAT file intensity values of the pixels in the feature.
CELIntensityStdev	float	linear_scale	SpecializedQuantitationType				The standard deviation of the intensity of the probe.
CELMask	boolean	linear_scale	SpecializedQuantitationType				A flag indicating that the probe was masked by the user.
CELOutlier	boolean	linear_scale	SpecializedQuantitationType				A flag indicating that the software called this probe an outlier.
CELPixels	integer	linear_scale	SpecializedQuantitationType				The number of pixels used to calculate the intensity.
CELX	integer	linear_scale	SpecializedQuantitationType				The x coordinate of the probe.
CELY	integer	linear_scale	SpecializedQuantitationType				The y coordinate of the probe.
CHPAbsCall	string_datatype	unscaled	PresentAbsent				The call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M).
CHPAllele	string_datatype	unscaled	SpecializedQuantitationType				The allele call in a SNP analysis: AA, BB, AB, AB_A, AB_B, or "No call".
CHPAllelePvalue	float	linear_scale	PValue		CHPAllele		The p-value calculated for a given allele call.
CHPAllelePvalueAA	float	linear_scale	PValue		CHPAllele		The p-value calculated for a given AA allele call.
CHPAllelePvalueAB	float	linear_scale	PValue		CHPAllele		The p-value calculated for a given AB allele call.
CHPAllelePvalueBB	float	linear_scale	PValue		CHPAllele		The p-value calculated for a given BB allele call.
CHPAllelePvalueNoCall	float	linear_scale	PValue		CHPAllele		The p-value calculated for a given NoCall allele call.
CHPAlleleRAS1	float	linear_scale	SpecializedQuantitationType				
CHPAlleleRAS2	float	linear_scale	SpecializedQuantitationType				
CHPAvgDiff	float	linear_scale	DerivedSignal				Average intensity difference
CHPAvgDiffChange	float	linear_scale	SpecializedQuantitationType				The change in average difference
CHPBaselineAbsent	float	linear_scale	SpecializedQuantitationType				Flag indicating if the baseline call was absent.
CHPChange	string_datatype	unscaled	PresentAbsent				A call indicating an Increase (I), Marginal Increase (MI), No Change (NC), Decrease (D), or Marginal Decrease (MD) in transcript level between a baseline array and an experiment array. May also have the value "No Call".
CHPChangePvalue	float	linear_scale	PValue		CHPChange		Measures the probability that the expression levels of a probe set in two different arrays are the same or not. When the p-value is close to 0.5 they are likely to be the same. When the p-value is close to 0 the expression level in the experiment array is
CHPCommonPairs	integer	linear_scale	SpecializedQuantitationType				The number of common probe pairs on two arrays (experiment versus baseline) after saturation across the probe set is determined.
CHPDPos-DNegRatio	float	linear_scale	Ratio				The ratio of the change in positive to the change in negative pairs
CHPDec	integer	linear_scale	SpecializedQuantitationType				The number of decreasing pairs
CHPDecRatio	float	linear_scale	Ratio				The ratio of decreasing pairs to the total number of pairs.
CHPDetection	string_datatype	unscaled	PresentAbsent				A measurement indicating if the transcript was detected (Present), not detected (Absent) or marginally detected (Marginal). Can be one of "A", "M", "P" or "No Call".
CHPDetectionPvalue	float	linear_scale	PValue		CHPDetection		See Detection p-value
CHPDiffCall	string_datatype	unscaled	PresentAbsent				The comparison change call
CHPFoldChange	float	linear_scale	Ratio				The fold change
CHPInc	integer	linear_scale	SpecializedQuantitationType				The number of increasing pairs.
CHPIncDecRatio	float	linear_scale	Ratio				The ratio of increase to decrease pairs.
CHPIncRatio	float	linear_scale	Ratio				The ratio of increasing pairs to the total number of pairs
CHPLogAvg	float	log_base_10	DerivedSignal				Average log ratio
CHPLogAvgRatioChange	float	log_base_10	SpecializedQuantitationType				The change in log average ratio
CHPNegChange	integer	linear_scale	SpecializedQuantitationType				The change in negative pairs
CHPNegative	integer	linear_scale	SpecializedQuantitationType				Number of negative probe pairs
CHPPairs	integer	linear_scale	SpecializedQuantitationType				The number of probe pairs in the probe set.
CHPPairsInAvg	integer	linear_scale	SpecializedQuantitationType				Number of probe pairs used in computing the average intensity difference
CHPPairsUsed	integer	linear_scale	SpecializedQuantitationType				The number of probe pairs in the probe set used in the Detection call.
CHPPosChange	float	linear_scale	SpecializedQuantitationType				The change in positive pairs.
CHPPosFraction	float	linear_scale	Ratio				The fraction of positive pairs
CHPPosNegRatio	float	linear_scale	Ratio				The ratio of the positive to the negative pairs
CHPPositive	integer	linear_scale	SpecializedQuantitationType				Number of positive probe pairs
CHPSignal	float	linear_scale	DerivedSignal				A measure of the relative abundance of a transcript.
CHPSignalLogRatio	float	log_base_2	Ratio				The change in expression level for a transcript between a baseline and an experiment array. This change is expressed as the Log2 ratio.
CHPSignalLogRatioHigh	float	log_base_2	Ratio				The upper limit of the Signal Log Ratio within a 95% confidence interval.
CHPSignalLogRatioLow	float	log_base_2	Ratio				The lower limit of the Signal Log Ratio within a 95% confidence interval.
CHPSortScore	float	linear_scale	SpecializedQuantitationType				The sort score.
ProbeSetName	string_datatype	unscaled	SpecializedQuantitationType				The name of the probe set.
Stat Pairs	integer	linear_scale	SpecializedQuantitationType				The number of probe pairs in the probe set.
Stat Pairs Used	integer	linear_scale	SpecializedQuantitationType				The number of probe pairs in the probe set used in the Detection call.
>>>AppliedBiosystems[Celera]							
Assay_Normalized_Signal	float		DerivedSignal				
CV	float		SpecializedQuantitationType				
Flags	integer	unscaled	SpecializedQuantitationType				
SDEV	float	linear_scale	MeasuredSignal				
S_N	float		SpecializedQuantitationType				
Signal	float	linear_scale	MeasuredSignal				
>>>ArrayGauge[FUJIFILM]							
Dens.(Total PSL)	float	linear_scale	MeasuredSignal	0			Total phospho stimulated luminescence.
Norm Data	float	log_base_2	DerivedSignal				
Overshining Status	boolean	unscaled	SpecializedQuantitationType				During quantification the analysis spots that display false positive intensity due to non-specific signal from neighboring clones are excluded.
Total PSL	float	linear_scale	SpecializedQuantitationType	0			Total phospho stimulated luminescence.
>>>ArrayVision[Imaging Research]							
% At Ceiling - Bkgd_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Clipped pixels - A quality control measure that reports the proportion of pixels at the uppermost limit (ceiling) of the density scale. The presence of clipped pixels suggest a problem during image formation, and can affect the validity of density data. V
% At Ceiling - Bkgd_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Clipped pixels - A quality control measure that reports the proportion of pixels at the uppermost limit (ceiling) of the density scale. The presence of clipped pixels suggest a problem during image formation, and can affect the validity of density data. V
% At Ceiling_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Clipped pixels - A quality control measure that reports the proportion of pixels at the uppermost limit (ceiling) of the density scale. The presence of clipped pixels suggest a problem during image formation, and can affect the validity of density data.
% At Ceiling_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Clipped pixels - A quality control measure that reports the proportion of pixels at the uppermost limit (ceiling) of the density scale. The presence of clipped pixels suggest a problem during image formation, and can affect the validity of density data.
% At Floor - Bkgd_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Clipped pixels - A quality control measure that reports the proportion of pixels at the lowermost limit (floor) of the density scale. The presence of clipped pixels suggest a problem during image formation, and can affect the validity of density data. Val
% At Floor - Bkgd_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Clipped pixels - A quality control measure that reports the proportion of pixels at the lowermost limit (floor) of the density scale. The presence of clipped pixels suggest a problem during image formation, and can affect the validity of density data. Val
% At Floor_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Clipped pixels - A quality control measure that reports the proportion of pixels at the lowermost limit (floor) of the density scale. The presence of clipped pixels suggest a problem during image formation, and can affect the validity of density data.
% At Floor_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Clipped pixels - A quality control measure that reports the proportion of pixels at the lowermost limit (floor) of the density scale. The presence of clipped pixels suggest a problem during image formation, and can affect the validity of density data.
% Replaced (AR VOL)_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Percentage of pixels replaced with estimated values in the calculation of AR volume.
% Replaced (AR VOL)_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Percentage of pixels replaced with estimated values in the calculation of AR volume.
AR VOL - RFU_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Artifact-removed density value for each spot, multiplied by its area.
AR VOL - RFU_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Artifact-removed density value for each spot, multiplied by its area.
Area - 5m2_Cy3	integer	linear_scale	SpecializedQuantitationType			Cy3	Area of the spot, background and/or reference region.
Area - 5m2_Cy5	integer	linear_scale	SpecializedQuantitationType			Cy5	Area of the spot, background and/or reference region.
Area - mm2_Cy3	integer	linear_scale	SpecializedQuantitationType			Cy3	Area of the spot, background and/or reference region.
Area - mm2_Cy5	integer	linear_scale	SpecializedQuantitationType			Cy5	Area of the spot, background and/or reference region.
Area - %G�%@m2_Cy3		linear_scale	SpecializedQuantitationType			Cy3	Area of the spot, background and/or reference region.
Area - %G�%@m2_Cy5		linear_scale	SpecializedQuantitationType			Cy5	Area of the spot, background and/or reference region.
Bkgd_Cy3	float	linear_scale	MeasuredSignal	1		Cy3	Background density or volume; background volume value is adjusted to the size of spot, where applicable.
Bkgd_Cy5	float	linear_scale	MeasuredSignal	1		Cy5	Background density or volume; background volume value is adjusted to the size of spot, where applicable.
Flag_Cy3	boolean	linear_scale	PresentAbsent			Cy3	Select this measure to manually flag data in the data table. The value of this measure can be 0 or 1.
Flag_Cy5	boolean	linear_scale	PresentAbsent			Cy5	Select this measure to manually flag data in the data table. The value of this measure can be 0 or 1.
MAD - RFU / 5m2_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Median of absolute deviation - median of the absolute values of deviations from the median density (i.e., the absolute values of pixel densities  median density); it is a measure of the variation around the median density value of the spot.
MAD - RFU / 5m2_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Median of absolute deviation - median of the absolute values of deviations from the median density (i.e., the absolute values of pixel densities  median density); it is a measure of the variation around the median density value of the spot.
MAD - RFU / mm2_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Median of absolute deviation - median of the absolute values of deviations from the median density (i.e., the absolute values of pixel densities  median density); it is a measure of the variation around the median density value of the spot.
MAD - RFU / mm2_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Median of absolute deviation - median of the absolute values of deviations from the median density (i.e., the absolute values of pixel densities  median density); it is a measure of the variation around the median density value of the spot.
MAD - RFU / %G�%@m2_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Median of absolute deviation - median of the absolute values of deviations from the median density (i.e., the absolute values of pixel densities  median density); it is a measure of the variation around the median density value of the spot.
MAD - RFU / %G�%@m2_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Median of absolute deviation - median of the absolute values of deviations from the median density (i.e., the absolute values of pixel densities  median density); it is a measure of the variation around the median density value of the spot.
Median Dens - Levels_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Median Density value of the spot Levels. ['Gray levels' (Levels) are the raw pixel intensity values upon which all other density/intensity scales are based.]
Median Dens - Levels_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Median Density value of the spot Levels. ['Gray levels' (Levels) are the raw pixel intensity values upon which all other density/intensity scales are based.]
Median Dens - RFU / %G�%@m2_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	
Median Dens - RFU / %G�%@m2_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	
S/N_Cy3	float	linear_scale	Ratio	1		Cy3	Signal-to-noise ratio - spot density minus background density, divided by the SD of the background density.
S/N_Cy5	float	linear_scale	Ratio	1		Cy5	Signal-to-noise ratio - spot density minus background density, divided by the SD of the background density.
SD - Levels_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Standard deviation of the pixel Levels values.
SD - Levels_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Standard deviation of the pixel Levels values.
SD - RFU / 5m2_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Standard deviation of the pixel density values.
SD - RFU / 5m2_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Standard deviation of the pixel density values.
SD - RFU / mm2_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Standard deviation of the pixel density values.
SD - RFU / mm2_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Standard deviation of the pixel density values.
SD - RFU / %G�%@m2_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Standard deviation of the pixel density values.
SD - RFU / %G�%@m2_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Standard deviation of the pixel density values.
SPOTLABEL							
Spot labels	integer	linear_scale	SpecializedQuantitationType				
VOL - Levels x mm2_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	
VOL - Levels x mm2_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	
sARMDens_Cy3	float	linear_scale	MeasuredSignal			Cy3	Background corrected ARM Density value. ARM Density value of the spot, minus the background Density value.
sARMDens_Cy5	float	linear_scale	MeasuredSignal			Cy5	Background corrected ARM Density value. ARM Density value of the spot, minus the background Density value.
sARVOL_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Subtracted AR volume value (AR volume value of the spot minus the background volume value); the background value is adjusted to the size of the spot when applicable.
sARVOL_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Subtracted AR volume value (AR volume value of the spot minus the background volume value); the background value is adjusted to the size of the spot when applicable.
sMedianDens_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Background corrected Median Density value. Median Density value of the spot, minus the background Density value.
sMedianDens_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Background corrected Median Density value. Median Density value of the spot, minus the background Density value.
sVOL_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Background corrected Volume value. Volume value of the spot, minus the background Volume value. The background value is adjusted to the size of the spot when applicable. sVOL = DxA_data - ((DxA_bkgd * Area_data)/Area_bkgd)).
sVOL_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Background corrected Volume value. Volume value of the spot, minus the background Volume value. The background value is adjusted to the size of the spot when applicable. sVOL = DxA_data - ((DxA_bkgd * Area_data)/Area_bkgd)).
>>>BZScan[TAGC ERM206]							
Diameter	float	linear_scale	SpecializedQuantitationType				Automatically computed spot diameter.
Fit_correction	float	linear_scale	SpecializedQuantitationType	1			Background level by unit surface.
Overshining_correction	float	linear_scale	SpecializedQuantitationType				Correction for overshining by unit radius.
Q(fit,const)	float	linear_scale	SpecializedQuantitationType				Spot intensity based on user-provided diameter and theoretical fit to the data.
Q(fit,var)	float	linear_scale	SpecializedQuantitationType				Spot intensity based on computed diameter and and theoretical fit to the data.
Q(image,const)	float	linear_scale	MeasuredSignal				Spot intensity based on user-provided diameter and measured data.
Q(image,var)	float	linear_scale	SpecializedQuantitationType				Spot intensity based on computed diameter and measured data.
QM	float	linear_scale	PValue		Q(image,const)		Quality metric: distance between measured data and theoretical fit.
SpotQuality	boolean	unscaled	PresentAbsent				Present/Absent (automatic guess).
>>>BeadStudio[Illumina]							
MIN_Signal	float	linear_scale	SpecializedQuantitationType				Minimum intensity of the Bead Type/target in the group.
AVG_Signal	float	linear_scale	MeasuredSignal				Average intensity of the Bead Type/target in the group.
MAX_Signal	float	linear_scale	SpecializedQuantitationType				Maximum intensity of the Bead Type/target in the group.
NARRAYS	integer	linear_scale	SpecializedQuantitationType				Number of samples in the group.
ARRAY_STDEV			SpecializedQuantitationType				Standard deviation associated with sample-to-sample variability within the group (undefined when the group contains a single sample).
BEAD_STDEV	float	linear_scale	Error		AVG_Signal		Average standard deviation associated with bead-to-bead variability for the samples in the group.
Avg_NBEADS	integer	linear_scale	SpecializedQuantitationType				Average number of beads per bead type representing probes for the gene.
Detection	float		SpecializedQuantitationType				1-p-value computed from the background model characterizing the chance that the target sequence signal was distinguishable from the negative controls.
Detection Pval	float		SpecializedQuantitationType				
DiffScore	float		SpecializedQuantitationType				Statistical confidence that the gene's expression has changed with respect to a reference group.
Concordance	float		SpecializedQuantitationType				Number of probes showing upregulated signal compared to the number of probes showing downregulated signal.
>>>BlueFuse[BlueGnome]							
AMPCH1	float	linear_scale	MeasuredSignal			Cy3	Total signal in Cy3 channel.
AMPCH2	float	linear_scale	MeasuredSignal			Cy5	Total signal in Cy5 channel.
AUTO EXCL	string_datatype	unscaled	SpecializedQuantitationType				Indication of whether a spot has been automatically excluded. Yes - it has been excluded, no - it has not been excluded.
BLOCK	integer	linear_scale	SpecializedQuantitationType				The sequential number of the block on the array.
CIRCULARITY	float	linear_scale	SpecializedQuantitationType				Estimate of the circularity of the spot, between 0 and 1. The nearer to 1, the more circular the spot.
CONFIDENCE	float	linear_scale	SpecializedQuantitationType				The Confidence Estimate in the calculated ratio, between 0 and 1.
FLAG	string_datatype	unscaled	SpecializedQuantitationType				The Confidence Flag calculated from the Confidence Estimate.
GRID OFFSET	float	linear_scale	SpecializedQuantitationType				Distance in pixels of the spot from the ideal grid position.
ID	string_datatype	unscaled	SpecializedQuantitationType				The ID of the spot, taken from ID field in GAL file.
LOG10PRODUCT	float	log_base_10	SpecializedQuantitationType				Log base 10 of the product of total signal in Cy3 channel multiplied by total signal in Cy5 channel.
LOG10RATIO CH1/CH2	float	log_base_10	SpecializedQuantitationType				Log base 10 of the ratio of total signal in Cy3 channel divided by total signal in Cy5 channel.
LOG10RATIO CH2/CH1	float	log_base_10	SpecializedQuantitationType				Log base 10 of the ratio of total signal in Cy5 channel divided by total signal in Cy3 channel.
LOG10SUM	float	log_base_10	SpecializedQuantitationType				Log base 10 of the sum of total signal in Cy3 channel plus total signal in Cy5 channel.
LOG2PRODUCT	float	log_base_2	SpecializedQuantitationType				Log base 2 of the product of total signal in Cy3 channel multiplied by total signal in Cy5 channel.
LOG2RATIO CH1/CH2	float	log_base_2	Ratio				Log base 2 of the ratio of total signal in Cy3 channel divided by total signal in Cy5 channel.
LOG2RATIO CH2/CH1	float	log_base_2	SpecializedQuantitationType				Log base 2 of the ratio of total signal in Cy5 channel divided by total signal in Cy3 channel.
LOG2SUM	float	log_base_2	SpecializedQuantitationType				Log base 2 of the sum of total signal in Cy3 channel plus total signal in Cy5 channel.
MAN EXCL	string_datatype	unscaled	SpecializedQuantitationType				Indication of whether a spot has been manually excluded. Yes - it has been manually excluded, no - it has not been manually excluded.
NAME	string_datatype	unscaled	SpecializedQuantitationType				The name of the spot, taken from Name field in GAL file.
P ON CH1	float	linear_scale	SpecializedQuantitationType			Cy3	Estimate of whether there is a biological signal in Cy3 channel, between 0 and 1.
P ON CH2	float	linear_scale	SpecializedQuantitationType			Cy5	Estimate of whether there is a biological signal in Cy5 channel, between 0 and 1.
PELCOL	integer	linear_scale	SpecializedQuantitationType				Calculated horizontal position of the spot on image in pixels. 1 is the left column of pixels.
PELROW	integer	linear_scale	SpecializedQuantitationType				Calculated vertical position of the spot on image in pixels. 1 is the top row of pixels.
PRODUCT	float	linear_scale	SpecializedQuantitationType				Product of total signal in Cy3 channel multiplied by total signal in Cy5 channel.
QUALITY			SpecializedQuantitationType				
RADIUS	float	linear_scale	SpecializedQuantitationType				Estimate of the radius of the spot in pixels.
RATIO CH1/CH2	float	linear_scale	SpecializedQuantitationType				Ratio of total signal in Cy3 channel divided by total signal channel in Cy5 channel.
RATIO CH2/CH1	float	linear_scale	SpecializedQuantitationType				Ratio of total signal in Cy5 channel divided by total signal channel in Cy3 channel.
SPOTNUM	integer	linear_scale	SpecializedQuantitationType				The sequential number of the spot on the array.
SUM	float	linear_scale	SpecializedQuantitationType				Sum of total signal in Cy3 channel plus total signal in Cy5 channel.
UNIFORMITY	float	linear_scale	SpecializedQuantitationType				Estimate of the uniformity of the spot, between 0 and 1. The nearer to 1 the more coin-shaped the spot, i.e. vertical sides and horizontal surface.
>>>ChipSkipper[EMBL]							
Comment	string_datatype	unscaled	SpecializedQuantitationType				Additional description of spot.
Comp_Channel Cy3	float	linear_scale	DerivedSignal			Cy3	Normalised intensity of Cy3_Vol-BG.
Comp_Channel Cy5	float	linear_scale	DerivedSignal			Cy5	Normalised intensity of Cy5_Vol-BG.
Comp_Directional_Ratio-Cy5/Cy3	float	linear_scale	SpecializedQuantitationType				Compensated directional ratio: if Comp_Ratio > 1 then Directional = Ratio, if Ratio < 1 then Directional = -1/Ratio.
Comp_Log2_Ratio	float	log_base_2	SpecializedQuantitationType				Compensated Log2 ratio: log2 (Comp_Ratio-Cy5/Cy3).
Comp_Ratio-Cy5/Cy3	float	linear_scale	Ratio				Compensated ratio ( = Comp_Channel Cy5 / Comp_Channel Cy3 ).
Cy3_Av-Vol/pixel	float	linear_scale	SpecializedQuantitationType			Cy3	Average intensity per pixel in color channel Cy3.
Cy3_BG-Arith	float	linear_scale	SpecializedQuantitationType	1		Cy3	Arithmetic average for local background in color channel Cy3.
Cy3_BG-Geom	float	linear_scale	SpecializedQuantitationType	1		Cy3	Geometric average for local background in color channel Cy3.
Cy3_BG-Median	float	linear_scale	SpecializedQuantitationType	1		Cy3	Median average for local background in color channel Cy3.
Cy3_BG_Tot	float	linear_scale	MeasuredSignal	1		Cy3	Total integrated background in color channel Cy3.
Cy3_SNR1	float	linear_scale	Error		Cy3_Vol-BG	Cy3	Sdev of local background average in color channel Cy3.
Cy3_SNR1_Score	float	linear_scale	Error		Cy3_Vol-BG	Cy3	Quality value based on intensity and background for color channel Cy3 (range: 0 = bad....1 = good).
Cy3_Sat-pixel	float	linear_scale	SpecializedQuantitationType			Cy3	Number of saturated pixel in color channel Cy3.
Cy3_Spot-area	float	linear_scale	SpecializedQuantitationType			Cy3	Area of spot in colour channel Cy3 in pixels.
Cy3_Vol-BG	float	linear_scale	SpecializedQuantitationType	1		Cy3	Background reduced intensity of colour channel Cy3.
Cy3_Volume	integer	linear_scale	MeasuredSignal			Cy3	Total integrated signal intensity in color channel Cy3.
Cy5_Av-Vol/pixel	float	linear_scale	SpecializedQuantitationType			Cy5	Average intensity per pixel in color channel Cy5.
Cy5_BG-Arith	float	linear_scale	SpecializedQuantitationType	1		Cy5	Arithmetic average for local background in color channel Cy5.
Cy5_BG-Geom	float	linear_scale	SpecializedQuantitationType	1		Cy5	Geometric average for local background in color channel Cy5.
Cy5_BG-Median	float	linear_scale	SpecializedQuantitationType	1		Cy5	Median average for local background in color channel Cy5.
Cy5_BG_Tot	float	linear_scale	MeasuredSignal	1		Cy5	Total integrated background in color channel Cy5.
Cy5_SNR1	float	linear_scale	Error		Cy5_Vol-BG	Cy5	Sdev of local background average in color channel Cy5.
Cy5_SNR1_Score	float	linear_scale	Error		Cy5_Vol-BG	Cy5	Quality value based on intensity and background for color channel Cy5 (range: 0 = bad....1 = good).
Cy5_Sat-pixel	float	linear_scale	SpecializedQuantitationType			Cy5	Number of saturated pixel in color channel Cy5.
Cy5_Spot-area	float	linear_scale	SpecializedQuantitationType			Cy5	Area of spot in colour channel Cy5 in pixels.
Cy5_Vol-BG	float	linear_scale	SpecializedQuantitationType	1		Cy5	Background reduced intensity of colour channel Cy5.
Cy5_Volume	integer	linear_scale	MeasuredSignal			Cy5	Total integrated signal intensity in color channel Cy5.
Directional_Ratio-Cy5/Cy3	float	linear_scale	SpecializedQuantitationType				Directional ratio: if Ratio > 1 then Directional = Ratio, if Ratio < 1 then Directional = -1/Ratio.
Flags	string_datatype	unscaled	SpecializedQuantitationType				Quality Flags: SNR1,SNR2 = low signal quality in color channel Cy5, Cy3; GS = low geometric score; MB = manually flagged bad.
GS_Flags	string_datatype	linear_scale	SpecializedQuantitationType				P = pass or M = marginal flag.
Group name	string_datatype	unscaled	SpecializedQuantitationType				Group name for this spot.
Image-x-Pos	integer	linear_scale	SpecializedQuantitationType				Image coordinate of spot.
Image-y-Pos	integer	linear_scale	SpecializedQuantitationType				Image coordinate of spot.
Line_Counter	integer	unscaled	SpecializedQuantitationType				Line counter
Log2_Ratio-Cy5/Cy3	float	log_base_2	Ratio				Log2 ratio: log2 (Ratio-Cy5/Cy3)
Median of ratios	float	linear_scale	SpecializedQuantitationType				Median of ratios (Cy5/Cy3) from all pixel in this spot.
Median of ratios % SDev	float	linear_scale	SpecializedQuantitationType				Standard deviation of Median of ratios in percent.
Ratio of medians	float	linear_scale	SpecializedQuantitationType				Ratio of Medians (Cy5/Cy3) from all pixel in this spot.
Ratio of medians % SDev	float	linear_scale	SpecializedQuantitationType				Standard deviation of Ratio of medians in percent.
Ratio-Cy5/Cy3	float	linear_scale	SpecializedQuantitationType				Direct ratio ( = Cy5_Vol-BG / Cy3_Vol-BG )
Regulation	string_datatype	unscaled	SpecializedQuantitationType				If Flag = SNR1 then Regulation=>Down; if Flag = SNR2 then Regulation=>up; if Flag = SNR1 AND SNR2 then Regulation=>weak; else Regulation = Ratio-Cy5/Cy3.
Rep_vol_BG2	float	linear_scale	SpecializedQuantitationType				Average of background reduced volume for onchip replicas (when calculated).
Replicas	float	linear_scale	SpecializedQuantitationType				
SNR*GS	float	linear_scale	SpecializedQuantitationType				Number of saturated pixel in both colors (logical or).
SNR-tot	float	linear_scale	SpecializedQuantitationType				Squared average of Cy5_SNR and Cy3_SNR.
SNR-tot_Score	float	linear_scale	SpecializedQuantitationType				Squared average of Cy5_%SNR and Cy3_%SNR.
Tot_Sat-pixel	float	linear_scale	SpecializedQuantitationType				Number of saturated pixel in color channel Cy5 OR color channel Cy3.
>>>CodeLink[Motorola Life Sciences]							
Cy3 BG Mean	float	linear_scale	MeasuredSignal	1		Cy3	Background mean in Cy3 channel.
Cy3 BG Median	integer	linear_scale	SpecializedQuantitationType	1		Cy3	Background median in Cy3 channel.
Cy3 Mean	float	linear_scale	SpecializedQuantitationType			Cy3	Statistical mean (average) of the raw intensity signal (i.e. mean of all the pixels belonging to the feature region) in Cy3 channel.
Cy3 Raw Intensity	float	linear_scale	MeasuredSignal			Cy3	The signal from the spot minus the median background in Cy3 channel.
Cy5 BG Mean	float	linear_scale	MeasuredSignal	1		Cy5	Background mean in Cy5 channel.
Cy5 BG Median	integer	linear_scale	SpecializedQuantitationType	1		Cy5	Background median in Cy5 channel.
Cy5 Mean	float	linear_scale	SpecializedQuantitationType			Cy5	Statistical mean (average) of the raw intensity signal (i.e. mean of all the pixels belonging to the feature region) in Cy5 channel.
Cy5 Raw Intensity	float	linear_scale	MeasuredSignal			Cy5	The signal from the spot minus the median background in Cy5 channel.
Flag	boolean	unscaled	SpecializedQuantitationType				Flag indicates if the spot matched with quality measures (i.e shape, low signal, saturated). TRUE corresponds to features that have to be discarded according to the quality measures, while FALSE is the opposite.
>>>Spot[CSIRO]							
# These first are just feature coordinate/index columns, and should be discarded.							
#indexs							The index of the spot.
#grid_r							The row index of the grid.
#grid_c							The column index of the grid.
#spot_r							The row index of the spot within the its grid.
#spot_c							The column index of the spot within the its grid.
area	integer	linear_scale	SpecializedQuantitationType				The number of pixels in the segmented spot.
Gmean	float	linear_scale	SpecializedQuantitationType	0		Cy3	The average pixel value within the spot: green band.
Gmedian	float	linear_scale	MeasuredSignal	0		Cy3	The median pixel value within the spot: green band.
GIQR	float			0		Cy3	The interquartile range of the logged pixel values within the spot: green band.
Rmean	float	linear_scale	SpecializedQuantitationType	0		Cy5	The average pixel value within the spot: red band.
Rmedian	float	linear_scale	MeasuredSignal	0		Cy5	The median pixel value within the spot: red band.
RIQR	float			0		Cy5	The interquartile range of the logged pixel values within the spot: red band.
bg.Gmean	float	linear_scale	SpecializedQuantitationType	1		Cy3	The average pixel value in the background region: green band.
bg.Gmedian	float	linear_scale	MeasuredSignal	1		Cy3	The median pixel value in the background region: green band.
bg.Gsd	float			1		Cy3	
bg.GIQR	float			1		Cy3	The interquartile range of the logged pixel values in the background region: green band.
bg.Rmean	float	linear_scale	SpecializedQuantitationType	1		Cy5	The average pixel value in the background region: red band.
bg.Rmedian	float	linear_scale	MeasuredSignal	1		Cy5	The median pixel value in the background region: red band.
bg.Rsd	float			1		Cy5	
bg.RIQR	float			1		Cy5	The interquartile range of the logged pixel values in the background region: red band.
valleyG			SpecializedQuantitationType			Cy3	Median of median image values in four neighbouring "valley" regions: green band. "Valley" regions are square regions between spots.
valleyR			SpecializedQuantitationType			Cy5	Median of median image values in four neighbouring "valley" regions: red band.
morphG	integer	linear_scale	SpecializedQuantitationType			Cy3	Value of a morphological opening of the green band image at the nominal spot centre. Openings and erosions (see below) use a rectangular structuring element with side lengths equal to twice the average horizontal and vertical distances between spots.
morphG.erode			SpecializedQuantitationType			Cy3	Value of a morphological erosion of the green band image at the nominal spot centre.
morphG.close.open	integer	linear_scale	SpecializedQuantitationType			Cy3	Value of a morphological closing followed by a morphological opening of the green band image at the nominal spot centre.
morphR 	integer	linear_scale	SpecializedQuantitationType			Cy5	Value of a morphological opening of the red band image at the nominal spot centre.
morphR.erode			SpecializedQuantitationType			Cy5	Value of a morphological erosion of the red band image at the nominal spot centre.
morphR.close.open	integer	linear_scale	SpecializedQuantitationType			Cy5	Value of a morphological closing followed by a morphological opening of the red band image at the nominal spot centre.
logratios	float	log_base_2	Ratio	0			The base-2 log of the background-adjusted ratio, R/G, using R/Gmedian for spot value and morphR/G for background.
perimeter	integer	linear_scale	SpecializedQuantitationType				The perimeter of the spot as measured by the number of pixels in the spot which have a neighbouring pixel outside the spot. Each pixel is considered to have 8 neighbours in this process.
circularity			SpecializedQuantitationType				A measure of circularity of the spot equal to area times four pi divided by perimeter squared. This is ideally one for circles and more than one for other shapes.
badspot			SpecializedQuantitationType				A flag which is one if the spot area is greater than the product of the horizontal and vertical average spot separations, and zero otherwise.
>>>CodeLink Expression Analysis[GE Healthcare]							
Raw_intensity	float	linear_scale	SpecializedQuantitationType	0			Spot density, which is the difference between the spot mean and the local background median.
Normalized_intensity	float	linear_scale	DerivedSignal	0			Normalized intensity value (the raw intensity divided by the normalization factor).
Quality_flag	string_datatype	unscaled	SpecializedQuantitationType	0			Metrics the software uses to indicate the quality of a spot.
Signal_strength	float	linear_scale	Ratio	0			Estimated signal above its local background noise level. The ratio is expressed as the spot mean divided by the local background standard deviation.
Spot_mean	float	linear_scale	MeasuredSignal	0			Sum of all pixel values in the spot area divided by the number of pixels.
Spot_median	integer	linear_scale	SpecializedQuantitationType	0			Median pixel intensity computed over the spot area.
Spot_stdev	float	linear_scale	Error	0	Spot_mean		Standard deviation of the pixel intensity in the spot.
Spot_area	integer	linear_scale	SpecializedQuantitationType	0			Number of pixels in the spot.
Spot_diameter	float	linear_scale	SpecializedQuantitationType	0			Spot diameter (in pixels) that the software calculates during data extraction.
Spot_noise_level	float	linear_scale	SpecializedQuantitationType	1			Local background noise level, given by the median signal of the pixels within the baackground ring.
Bkgd_mean	float	linear_scale	MeasuredSignal	1			Estimate of the background mean that the software computes, using the pixel intensities in the background area surrounding the spot.
Bkgd_median	integer	linear_scale	SpecializedQuantitationType	1			Estimate of the background median the software computes, using the pixel intensities inside the background area surrounding the spot.
Bkgd_stdev	float	linear_scale	Error	1	Bkgd_mean		Estimate of the background standard deviation that the software computes, using the pixel intensities inside the background area surrounding the spot.
Bkgd_area	float	linear_scale	SpecializedQuantitationType	1			Number of pixels that the software includes to compute the estimated local background mean, median, and standard deviation.
>>>Feature Extraction Software[Agilent Technologies]							
BGPixCorrelation	float	linear_scale	SpecializedQuantitationType				Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space. The covariance of two features measures their tendency to vary together, i.e. to co-vary. In this case, it is a cumulative quantitation of
BGSubSigCorrelation	float	linear_scale	SpecializedQuantitationType				Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space.
DyeNormCorrelation	float	linear_scale	SpecializedQuantitationType				Dye normalized red and green pixel correlation.
ErrorModel	integer	linear_scale	SpecializedQuantitationType				ErrorModel Indicates the error model that the user chose for feature extraction. A 0 indicates use of the Propogated Error Model. A 1 indicates use of the Universal Error Model.
Failed	boolean	linear_scale	Failed				Set to one if the quantitation values of a feature are considered bad enough to thrown out in the higher level analysis. Features are thrown out if both channels are saturated or if either channel is a non-uniform outlier. A feature can be failed from out
Green.BGPixSDev	float	linear_scale	Error		Green.Background	Cy3	
Green.Background	float	linear_scale	MeasuredSignal	1		Cy3	
Green.DerivedSignal	float	linear_scale	DerivedSignal			Cy3	
Green.DyeNormSignal	float	linear_scale	SpecializedQuantitationType			Cy3	
Green.MeasuredSignal	float	linear_scale	MeasuredSignal			Cy3	
Green.PixSDev	float	linear_scale	Error		Green.MeasuredSignal	Cy3	
Green.ProcessedSigError	float	linear_scale	Error		Green.DerivedSignal	Cy3	
HighEndCorrDNCorrelation	float	linear_scale	SpecializedQuantitationType				
HighEndDyeNormApplied	boolean	linear_scale	SpecializedQuantitationType				Has a value of 0 or 1.
IsManualFlag	boolean	linear_scale	SpecializedQuantitationType				If a feature has been moved manually this flag will be set to 1.
IsNormalization	boolean	linear_scale	SpecializedQuantitationType				A boolean flag which indicates if a feature is used to measure dye bias. A 1 incidates the value was used.
IsUsedBGAdjust	float	linear_scale	SpecializedQuantitationType				A boolean used to flag features used for computation of global BG offset. A 1 indicates the feature was used.
LogRatio	float	log_base_10	Ratio				log(REDsignal/GREENsignal) per feature. Signals in both channels are post dye normalization If SURROGATES are disabled, then this value will be set to: -2 if DyeNormRedSig &lt;= 0.0 &amp;DyeNormGreenSig > 0.0; 2 if DyeNormRedSig > 0.0 &amp; DyeNormGreenSi
LogRatioError	float	log_base_10	Error		LogRatio		LogRatioError = error of the log ratio calculated according to the error model chosen. If SURROGATES are disabled, then this value will be set to if DyeNormRedSig &lt;= 0.0 OR DyeNormGreenSig &lt;= 0.0
PValueLogRatio	float	percent	PValue		LogRatio		Significance level of the Log Ratio computed for a feature
PixCorrelation	float	linear_scale	SpecializedQuantitationType				Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space. The covariance of two features measures their tendency to vary together, i.e. to co-vary. In this case, it is a cumulative quantitation of
PositionX	float	linear_scale	SpecializedQuantitationType				Found X coordinate of the feature centroid currently reported in pixels.
PositionY	float	linear_scale	SpecializedQuantitationType				Found Y coordinate of the feature centroid currently reported in pixels.
Red.BGPixSDev	float	linear_scale	Error		Red.Background	Cy5	
Red.Background	float	linear_scale	MeasuredSignal	1		Cy5	
Red.DerivedSignal	float	linear_scale	DerivedSignal			Cy5	
Red.DyeNormSignal	float	linear_scale	SpecializedQuantitationType			Cy5	
Red.MeasuredSignal	float	linear_scale	MeasuredSignal			Cy5	
Red.PixSDev	float	linear_scale	Error		Red.MeasuredSignal	Cy5	
Red.ProcessedSigError	float	linear_scale	Error		Red.DerivedSignal	Cy5	
SpotExtentX	float	linear_scale	SpecializedQuantitationType				The size of a spot in X in microns.
SpotExtentY	float	linear_scale	SpecializedQuantitationType				The size of a spot in Y in microns.
gBGMeanSignal	float	linear_scale	MeasuredSignal	1		Cy3	Mean local background signal (local to corresponding feature) computed per channel.
gBGMedianSignal	float	linear_scale	SpecializedQuantitationType	1		Cy3	Median local background signal (local to corresponding feature) computed per channel.
gBGNumPix	integer	linear_scale	SpecializedQuantitationType	1		Cy3	Total number of pixels used to compute Local BG statistics per spot; ie. Total number of BG inlier pixels. This number is computed independently in each channel.
gBGPixSDev	float	linear_scale	Error	1	gBGMeanSignal	Cy3	Standard deviation of all inlier pixels per Local BG of each feature, computed independently in each channel.
gBGSDUsed	float	linear_scale	Error	1	gBGUsed	Cy3	Standard deviation of background used in green channel.
gBGSubSigError	float	linear_scale	Error		gBGSubSignal	Cy3	Propagated standard error as computed on net green background subtracted signal.
gBGSubSignal	float	linear_scale	SpecializedQuantitationType			Cy3	The net green signal following the subtraction of the background from the raw mean green signal.
gBGUsed	float	linear_scale	SpecializedQuantitationType	1		Cy3	Background value subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel.
gBackground	float	linear_scale	MeasuredSignal	1		Cy3	Mean local background signal (local to corresponding feature) computed per channel.
gDerivedSignal	float	linear_scale	DerivedSignal			Cy3	The propagated feature signal, per channel, used for computation of log ratio.
gDyeNormError	float	linear_scale	Error		gDyeNormSignal	Cy3	The standard error associated with the dye normalized signal.
gDyeNormSignal	float	linear_scale	SpecializedQuantitationType			Cy3	The dye normalized signal in the indicated channel.
gHighEndCorrDNError	float	linear_scale	Error		gHighEndCorrDNSig	Cy3	
gHighEndCorrDNSig	float	linear_scale	SpecializedQuantitationType			Cy3	
gIsBGNonUnifOL	boolean	linear_scale	SpecializedQuantitationType			Cy3	Boolean flag indicating if a background is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a "uniform" feature. A 1 indicates Feature is a non-uniformity outlier.
gIsBGPopnOL	boolean	linear_scale	SpecializedQuantitationType			Cy3	Boolean flag indicating if a background is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an u
gIsFeatNonUnifOL	boolean	linear_scale	SpecializedQuantitationType			Cy3	Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a "uniform" feature. A 1 indicates Feature is a non-uniformity outlier.
gIsFeatPopnOL	boolean	linear_scale	SpecializedQuantitationType			Cy3	Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an uppe
gIsFound	boolean	linear_scale	SpecializedQuantitationType			Cy3	A boolean used to flag found (strong) features. The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. NO
gIsInNegCtrlRange	boolean	linear_scale	SpecializedQuantitationType			Cy3	Boolean that identifies this spot as being in the range of background.
gIsPosAndSignif	boolean	linear_scale	SpecializedQuantitationType			Cy3	Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. Significance is established via a 2-sided t-test against the user-settable maximum p-value. A 1 indicates Feature i
gIsSaturated	boolean	linear_scale	SpecializedQuantitationType			Cy3	Boolean flag indicating if a feature is saturated or not. A feature is saturated if 50% of the pixels in a feature are above the saturation threshold. A value of 1 means saturated.
gIsWellAboveBG	boolean	linear_scale	SpecializedQuantitationType			Cy3	Boolean flag indicating if a feature is well above background or not. A feature must be gIsPosAndSignif and additionally the gBGSubSignal must be greater than 2.6*g(r)BG_SD. A 1 indicates a feature IsWellAboveBG.
gMeanSignal	float	linear_scale	MeasuredSignal			Cy3	Raw mean signal of feature in green channel.
gMeasuredSignal	float	linear_scale	MeasuredSignal			Cy3	Raw mean signal of feature in green channel.
gMedianSignal	float	linear_scale	SpecializedQuantitationType			Cy3	Raw median signal of feature in green channel.
gNetSignal	float	linear_scale	SpecializedQuantitationType			Cy3	The meanSignal - the scanner offset.
gNumBGUsed	integer	linear_scale	SpecializedQuantitationType	1		Cy3	A count of the number of background pixels used in the green channel.
gNumPix	integer	linear_scale	SpecializedQuantitationType			Cy3	Total number of pixels used to compute feature statistics; ie. total number of inlier pixels/per spot, computed independently in each channel. The number of inlier pixels are the same in both channels.
gNumPixOLHi	integer	linear_scale	SpecializedQuantitationType			Cy3	Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations.
gNumPixOLLo	integer	linear_scale	SpecializedQuantitationType			Cy3	Number of outlier pixels per feature with intensity &lt; lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extract
gNumSatPix	integer	linear_scale	SpecializedQuantitationType			Cy3	Total number of saturated pixels per feature, computed per channel.
gPValFeatEqBG	float	linear_scale	SpecializedQuantitationType			Cy3	P-value from t-test of significance between green Mean signal and green background.
gPixSDev	float	linear_scale	Error		gMeanSignal	Cy3	Standard deviation of all inlier pixels per feature; this is computed independently in each channel.
gProcessedSigError	float	linear_scale	Error		gProcessedSignal	Cy3	Standard error of propagated feature signal, per channel.
gProcessedSignal	float	linear_scale	DerivedSignal			Cy3	The propagated feature signal, per channel, used for computation of log ratio.
gSpatialDetrendIsInFilteredSet	boolean	linear_scale	SpecializedQuantitationType			Cy3	Set to true for a given feature if it is part of the filtered set used to fit the surface measuring the spatial trend across the microarray. This feature is considered part of the locally weighted x% of the features.
gSpatialDetrendSurfaceValue	float	linear_scale	SpecializedQuantitationType			Cy3	Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet.
gSurrogateUsed	float	linear_scale	SpecializedQuantitationType			Cy3	The green surrogate value used.
rBGMeanSignal	float	linear_scale	MeasuredSignal	1		Cy5	Mean local background signal (local to corresponding feature) computed per channel.
rBGMedianSignal	float	linear_scale	SpecializedQuantitationType	1		Cy5	Median local background signal (local to corresponding feature) computed per channel.
rBGNumPix	integer	linear_scale	SpecializedQuantitationType	1		Cy5	Total number of pixels used to compute Local BG statistics per spot; ie. Total number of BG inlier pixels. This number is computed independently in each channel.
rBGPixSDev	float	linear_scale	Error	1	rBGMeanSignal	Cy5	Standard deviation of all inlier pixels per Local BG of each feature, computed independently in each channel.
rBGSDUsed	float	linear_scale	Error	1	rBGUsed	Cy5	Standard deviation of background used in red channel.
rBGSubSigError	float	linear_scale	Error		rBGSubSignal	Cy5	Propagated standard error as computed on net red background subtracted signal.
rBGSubSignal	float	linear_scale	SpecializedQuantitationType			Cy5	The net red signal following the subtraction of the background from the raw mean red signal.
rBGUsed	float	linear_scale	SpecializedQuantitationType	1		Cy5	Background value subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel.
rBackground	float	linear_scale	MeasuredSignal	1		Cy5	Mean local background signal (local to corresponding feature) computed per channel.
rDerivedSignal	float	linear_scale	DerivedSignal			Cy5	The propagated feature signal, per channel, used for computation of log ratio.
rDyeNormError	float	linear_scale	Error		rDyeNormSignal	Cy5	The standard error associated with the dye normalized signal.
rDyeNormSignal	float	linear_scale	SpecializedQuantitationType			Cy5	The dye normalized signal in the indicated channel.
rHighEndCorrDNError	float	linear_scale	Error		rHighEndCorrDNSig	Cy5	
rHighEndCorrDNSig	float	linear_scale	SpecializedQuantitationType			Cy5	
rIsBGNonUnifOL	boolean	linear_scale	SpecializedQuantitationType			Cy5	Boolean flag indicating if a background is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a "uniform" feature. A 1 indicates Feature is a non-uniformity outlier.
rIsBGPopnOL	boolean	linear_scale	SpecializedQuantitationType			Cy5	Boolean flag indicating if a background is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an u
rIsFeatNonUnifOL	boolean	linear_scale	SpecializedQuantitationType			Cy5	Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a "uniform" feature. A 1 indicates Feature is a non-uniformity outlier.
rIsFeatPopnOL	boolean	linear_scale	SpecializedQuantitationType			Cy5	Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an uppe
rIsFound	boolean	linear_scale	SpecializedQuantitationType			Cy5	A boolean used to flag found (strong) features. The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. NO
rIsInNegCtrlRange	boolean	linear_scale	SpecializedQuantitationType			Cy5	Boolean that identifies this spot as being in the range of background.
rIsPosAndSignif	boolean	linear_scale	SpecializedQuantitationType			Cy5	Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. Significance is established via a 2-sided t-test against the user-settable maximum p-value. A 1 indicates Feature i
rIsSaturated	boolean	linear_scale	SpecializedQuantitationType			Cy5	Boolean flag indicating if a feature is saturated or not. A feature is saturated if 50% of the pixels in a feature are above the saturation threshold. A value of 1 means saturated.
rIsWellAboveBG	boolean	linear_scale	SpecializedQuantitationType			Cy5	Boolean flag indicating if a feature is well above background or not. A feature must be gIsPosAndSignif and additionally the gBGSubSignal must be greater than 2.6*g(r)BG_SD. A 1 indicates a feature IsWellAboveBG.
rMeanSignal	float	linear_scale	MeasuredSignal			Cy5	Raw mean signal of feature in red channel.
rMeasuredSignal	float	linear_scale	MeasuredSignal			Cy5	Raw mean signal of feature in red channel.
rMedianSignal	float	linear_scale	SpecializedQuantitationType			Cy5	Raw median signal of feature in red channel.
rNetSignal	float	linear_scale	SpecializedQuantitationType			Cy5	The meanSignal - the scanner offset.
rNumBGUsed	integer	linear_scale	SpecializedQuantitationType	1		Cy5	A count of the number of background pixels used in the red channel.
rNumPix	integer	linear_scale	SpecializedQuantitationType			Cy5	Total number of pixels used to compute feature statistics; ie. total number of inlier pixels/per spot, computed independently in each channel. The number of inlier pixels are the same in both channels.
rNumPixOLHi	integer	linear_scale	SpecializedQuantitationType			Cy5	Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations.
rNumPixOLLo	integer	linear_scale	SpecializedQuantitationType			Cy5	Number of outlier pixels per feature with intensity &lt; lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extract
rNumSatPix	integer	linear_scale	SpecializedQuantitationType			Cy5	Total number of saturated pixels per feature, computed per channel.
rPValFeatEqBG	float	linear_scale	SpecializedQuantitationType			Cy5	P-value from t-test of significance between red Mean signal and red background.
rPixSDev	float	linear_scale	Error		rMeanSignal	Cy5	Standard deviation of all inlier pixels per feature; this is computed independently in each channel.
rProcessedSigError	float	linear_scale	Error		rProcessedSignal	Cy5	Standard error of propagated feature signal, per channel.
rProcessedSignal	float	linear_scale	DerivedSignal			Cy5	The propagated feature signal, per channel, used for computation of log ratio.
rSpatialDetrendIsInFilteredSet	boolean	linear_scale	SpecializedQuantitationType			Cy5	Set to true for a given feature if it is part of the filtered set used to fit the surface measuring the spatial trend across the microarray. This feature is considered part of the locally weighted x% of the features.
rSpatialDetrendSurfaceValue	float	linear_scale	SpecializedQuantitationType			Cy5	Value of the smoothed surface derived from the set of features that are part of SpatialDetrendIsInFilteredSet.
rSurrogateUsed	float	linear_scale	SpecializedQuantitationType			Cy5	The red surrogate value used.
xDev	float	log_base_10	SpecializedQuantitationType				Used to compute the Log Ratio PValue.
>>>GEMTools[Incyte Genomics]							
BalancedDiffExpr	float	linear_scale	SpecializedQuantitationType				Balanced fold change.
CloneID	string_datatype	unscaled	SpecializedQuantitationType				Incyte identifier for individual clone spotted on the array.
CloneSource	string_datatype	unscaled	SpecializedQuantitationType				All arrayed elements were either clones derived from Incyte cDNA libraries, or sequences generated specifically to be used as hybridization and/or signal balancing controls.
DiffExpr	float	linear_scale	SpecializedQuantitationType				Unbalanced fold change.
GEMID	string_datatype	unscaled	SpecializedQuantitationType				Unique identifier.
GeneID	string_datatype	unscaled	SpecializedQuantitationType				Incyte unique identifier for a sequence contig.
GeneName	string_datatype	unscaled	SpecializedQuantitationType				Genbank annotation of Incyte sequence contig.
IncyteCloneID	string_datatype	unscaled	SpecializedQuantitationType				Incyte identifier for individual clone spotted on the array.
Location	integer	linear_scale	SpecializedQuantitationType				An Incyte code that can be used to determine the location of the spot on the array.
P1Area%	integer	linear_scale	SpecializedQuantitationType			Cy5	Area of spot coverage.
P1Description	string_datatype	unscaled	SpecializedQuantitationType			Cy5	Identifier or code name for Cy5 labeled probe.
P1S/B	float	linear_scale	SpecializedQuantitationType	1		Cy5	Element signal to background in the Cy5 channel.
P1Signal	integer	linear_scale	MeasuredSignal			Cy5	Signal intensity in the Cy5 channel.
P2Area%	integer	linear_scale	SpecializedQuantitationType			Cy3	Area of spot coverage.
P2BalancedSignal	integer	linear_scale	SpecializedQuantitationType				Balanced Cy3 signal (balanced by total average signal intensity in both channels).
P2Description	string_datatype	unscaled	SpecializedQuantitationType			Cy3	Identifier or code name for Cy3 labeled probe.
P2S/B	float	linear_scale	SpecializedQuantitationType	1		Cy3	Element signal to background in the Cy3 channel.
P2Signal	integer	linear_scale	MeasuredSignal			Cy3	Signal intensity in the Cy3 channel.
PCRStatus	string_datatype	unscaled	SpecializedQuantitationType				An indicator of the quality of the spotted cDNA.
Probe1	string_datatype	unscaled	SpecializedQuantitationType			Cy5	Unique identifier for Cy5 labeled probe.
Probe2	string_datatype	unscaled	SpecializedQuantitationType			Cy3	Unique identifier for Cy3 labeled probe.
>>>GLEAMS[NuTec Sciences]							
BG.Cy3	float	linear_scale	MeasuredSignal	1		Cy3	Median pixel intensity computed over the local background region for Cy3.
BG.Cy5	float	linear_scale	MeasuredSignal	1		Cy5	Median pixel intensity computed over the local background region for Cy5.
Mean.Sig.Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Pixel intensity averaged over the local signal region for Cy3.
Mean.Sig.Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Pixel intensity averaged over the local signal region for Cy5.
Med.Sig.Cy3	integer	linear_scale	MeasuredSignal			Cy3	Median pixel intensity computed over the local signal region for Cy3.
Med.Sig.Cy5	integer	linear_scale	MeasuredSignal			Cy5	Median pixel intensity computed over the local signal region for Cy5.
SD.Cy3	float	linear_scale	Error		Mean.Sig.Cy3	Cy3	Standard deviation of pixel intensities over the local signal region for Cy3.
SD.Cy5	float	linear_scale	Error		Mean.Sig.Cy5	Cy5	Standard deviation of pixel intensities over the local signal region for Cy5.
Sig.Area	integer	linear_scale	SpecializedQuantitationType				Number of pixels in the local signal region.
X	integer	linear_scale	SpecializedQuantitationType				Location of the center of the spot on the array on the X-axis.
Y	integer	linear_scale	SpecializedQuantitationType				Location of the center of the spot on the array on the Y-axis.
>>>GenePix[Axon Instruments]							
% > B595+1SD	integer	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 595 nm.
% > B595+2SD	integer	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 595 nm.
% > B685+1SD	integer	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 685 nm.
% > B685+2SD	integer	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 685 nm.
B595	integer	linear_scale	SpecializedQuantitationType	1		Cy3	The actual background value used for the feature in GenePix Pro calculations (as opposed to B595 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtrac
B595 CV	integer	linear_scale	SpecializedQuantitationType	1		Cy3	The coefficient of variation of local background pixel intensity.
B595 Mean	integer	linear_scale	MeasuredSignal	1		Cy3	The mean feature background intensity at wavelength 595 nm.
B595 Median	integer	linear_scale	SpecializedQuantitationType	1		Cy3	The median feature background intensity at wavelength 595 nm.
B595 SD	integer	linear_scale	Error	1	B595 Median	Cy3	The standard deviation of the feature background intensity at wavelength 595 nm.
B685	integer	linear_scale	SpecializedQuantitationType	1		Cy5	The actual background value used for the feature in GenePix Pro calculations (as opposed to B685 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtrac
B685 CV	integer	linear_scale	SpecializedQuantitationType	1		Cy5	The coefficient of variation of local background pixel intensity.
B685 Mean	integer	linear_scale	MeasuredSignal	1		Cy5	The mean feature background intensity at wavelength 685 nm.
B685 Median	integer	linear_scale	SpecializedQuantitationType	1		Cy5	The median feature background intensity at wavelength 685 nm.
B685 SD	integer	linear_scale	Error	1	B685 Median	Cy5	The standard deviation of the feature background intensity at wavelength 685 nm.
F595 % Sat.	integer	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels at wavelength 595 nm that are saturated.
F595 CV	integer	linear_scale	SpecializedQuantitationType			Cy3	The coefficient of variation of feature pixel intensity.
F595 Mean	integer	linear_scale	MeasuredSignal			Cy3	Mean feature pixel intensity at wavelength 595 nm.
F595 Mean - B595	integer	linear_scale	SpecializedQuantitationType			Cy3	The mean feature pixel intensity at wavelength 595 nm with the median background subtracted.
F595 Median	integer	linear_scale	SpecializedQuantitationType			Cy3	Median feature pixel intensity at wavelength 595 nm.
F595 Median - B595	integer	linear_scale	SpecializedQuantitationType			Cy3	The median feature pixel intensity at wavelength 595 nm with the median background subtracted.
F595 SD	integer	linear_scale	Error		F595 Median	Cy3	The standard deviation of the feature intensity at wavelength 595 nm.
F595 Total Intensity	integer	linear_scale	SpecializedQuantitationType			Cy3	The sum of feature pixel intensities at 595 nm.
F685 % Sat.	integer	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels at wavelength 685 nm that are saturated.
F685 CV	integer	linear_scale	SpecializedQuantitationType			Cy5	The coefficient of variation of feature pixel intensity.
F685 Mean	integer	linear_scale	MeasuredSignal			Cy5	Mean feature pixel intensity at wavelength 685 nm.
F685 Mean - B685	integer	linear_scale	SpecializedQuantitationType			Cy5	The mean feature pixel intensity at wavelength 685 nm with the median background subtracted.
F685 Median	integer	linear_scale	SpecializedQuantitationType			Cy5	Median feature pixel intensity at wavelength 685 nm.
F685 Median - B685	integer	linear_scale	SpecializedQuantitationType			Cy5	The median feature pixel intensity at wavelength 685 nm with the median background subtracted.
F685 SD	integer	linear_scale	Error		F685 Median	Cy5	The standard deviation of the feature intensity at wavelength 685 nm.
F685 Total Intensity	integer	linear_scale	SpecializedQuantitationType			Cy5	The sum of feature pixel intensities at 685 nm.
Log Ratio (685/595)	float	log_base_2	Ratio				Log (base 2) transform of the ratio of the medians.
Mean of Ratios (685/595)	float	linear_scale	SpecializedQuantitationType				The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Median of Ratios (685/595)	float	linear_scale	SpecializedQuantitationType				The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratio of Means (685/595)	float	linear_scale	SpecializedQuantitationType				The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Medians (685/595)	float	linear_scale	SpecializedQuantitationType				The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratios SD (685/595)	float	linear_scale	Error		Median of Ratios (685/595)		The geometric standard deviation of the pixel intensity ratios.
Rgn R2 (685/595)	float	linear_scale	SpecializedQuantitationType				The coefficient of determination for the current regression value.
Rgn Ratio (685/595)	float	linear_scale	SpecializedQuantitationType				The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
SNR 595	float	linear_scale	SpecializedQuantitationType	1		Cy5	The signal-to-noise ratio at 595 nm, defined by (F595 Mean - B595 Mean) / (B595 SD)
SNR 685	float	linear_scale	SpecializedQuantitationType	1		Cy5	The signal-to-noise ratio at 685 nm, defined by (F685 Mean - B685 Mean) / (B685 SD)
Sum of Means (685/595)	integer	linear_scale	SpecializedQuantitationType				The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Sum of Medians (685/595)	integer	linear_scale	SpecializedQuantitationType				The sum of the median intensities for each wavelength, with the median background subtracted.
% > B633+1SD	integer	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 633 nm.
% > B633+2SD	integer	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 633 nm.
B633	integer	linear_scale	SpecializedQuantitationType	1		Cy5	The actual background value used for the feature in GenePix Pro calculations (as opposed to B633 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtrac
B633 CV	integer	linear_scale	SpecializedQuantitationType	1		Cy5	The coefficient of variation of local background pixel intensity.
B633 Mean	integer	linear_scale	MeasuredSignal	1		Cy5	The mean feature background intensity at wavelength 633 nm.
B633 Median	integer	linear_scale	SpecializedQuantitationType	1		Cy5	The median feature background intensity at wavelength 633 nm.
B633 SD	integer	linear_scale	Error	1	B633 Median	Cy5	The standard deviation of the feature background intensity at wavelength 633 nm.
F633 % Sat.	integer	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels at wavelength 633 nm that are saturated.
F633 CV	integer	linear_scale	SpecializedQuantitationType			Cy5	The coefficient of variation of feature pixel intensity.
F633 Mean	integer	linear_scale	MeasuredSignal			Cy5	Mean feature pixel intensity at wavelength 633 nm.
F633 Mean - B633	integer	linear_scale	SpecializedQuantitationType			Cy5	The mean feature pixel intensity at wavelength 633 nm with the median background subtracted.
F633 Median	integer	linear_scale	SpecializedQuantitationType			Cy5	Median feature pixel intensity at wavelength 633 nm.
F633 Median - B633	integer	linear_scale	SpecializedQuantitationType			Cy5	The median feature pixel intensity at wavelength 633 nm with the median background subtracted.
F633 SD	integer	linear_scale	Error		F633 Median	Cy5	The standard deviation of the feature intensity at wavelength 633 nm.
F633 Total Intensity	integer	linear_scale	SpecializedQuantitationType			Cy5	The sum of feature pixel intensities at 633 nm.
Log Ratio (633/532)	float	log_base_2	Ratio				Log (base 2) transform of the ratio of the medians.
Mean of Ratios (633/532)	float	linear_scale	SpecializedQuantitationType				The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Median of Ratios (633/532)	float	linear_scale	SpecializedQuantitationType				The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratio of Means (633/532)	float	linear_scale	SpecializedQuantitationType				The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Medians (633/532)	float	linear_scale	SpecializedQuantitationType				The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratios SD (633/532)	float	linear_scale	Error		Median of Ratios (633/532)		The geometric standard deviation of the pixel intensity ratios.
Rgn R2 (633/532)	float	linear_scale	SpecializedQuantitationType				The coefficient of determination for the current regression value.
Rgn Ratio (633/532)	float	linear_scale	SpecializedQuantitationType				The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
SNR 633	float	linear_scale	SpecializedQuantitationType	1		Cy5	The signal-to-noise ratio at 633 nm, defined by (F633 Mean - B633 Mean) / (B633 SD)
Sum of Means (633/532)	integer	linear_scale	SpecializedQuantitationType				The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Sum of Medians (633/532)	integer	linear_scale	SpecializedQuantitationType				The sum of the median intensities for each wavelength, with the median background subtracted.
% > B532+1SD	integer	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.
% > B532+1SD2	integer	linear_scale	SpecializedQuantitationType			Cy3	
% > B532+2SD	integer	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.
% > B532+2SD2	integer	linear_scale	SpecializedQuantitationType			Cy3	
% > B563+1SD	integer	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 563 nm.
% > B563+2SD	integer	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 563 nm.
% > B635+1SD	integer	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.
% > B635+1SD2	integer	linear_scale	SpecializedQuantitationType			Cy5	
% > B635+2SD	integer	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 635 nm.
% > B635+2SD2	integer	linear_scale	SpecializedQuantitationType			Cy5	
Autoflag	boolean	linear_scale	SpecializedQuantitationType				Reports whether or not a feature has been flagged from the Flag Features dialog box. It applies to good and bad flags only.
B Pixels	integer	linear_scale	SpecializedQuantitationType				The total number of background pixels.
B532	integer	linear_scale	SpecializedQuantitationType	1		Cy3	The actual background value used for the feature in GenePix Pro calculations (as opposed to B532 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtrac
B532 CV	integer	linear_scale	SpecializedQuantitationType	1		Cy3	The coefficient of variation of local background pixel intensity.
B532 Mean	integer	linear_scale	MeasuredSignal	1		Cy3	The mean feature background intensity at wavelength 532 nm.
B532 Median	integer	linear_scale	SpecializedQuantitationType	1		Cy3	The median feature background intensity at wavelength 532 nm.
B532 SD	integer	linear_scale	Error	1	B532 Median	Cy3	The standard deviation of the feature background intensity at wavelength 532 nm.
B532 SD2	float	linear_scale	Error	1	B532 Median	Cy3	
B563 Mean	integer	linear_scale	MeasuredSignal	1		Cy3	The mean feature background intensity at wavelength 563 nm.
B563 Median	integer	linear_scale	SpecializedQuantitationType	1		Cy3	The median feature background intensity at wavelength 563 nm.
B563 SD	integer	linear_scale	Error	1	B563 Median	Cy3	The standard deviation of the feature background intensity at wavelength 563 nm.
B635	integer	linear_scale	SpecializedQuantitationType	1		Cy5	The actual background value used for the feature in GenePix Pro calculations (as opposed to B635 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtrac
B635 CV	integer	linear_scale	SpecializedQuantitationType	1		Cy5	The coefficient of variation of local background pixel intensity.
B635 Mean	integer	linear_scale	MeasuredSignal	1		Cy5	The mean feature background intensity at wavelength 635 nm.
B635 Median	integer	linear_scale	SpecializedQuantitationType	1		Cy5	The median feature background intensity at wavelength 635 nm.
B635 SD	integer	linear_scale	Error	1	B635 Median	Cy5	The standard deviation of the feature background intensity at wavelength 635 nm.
B635 SD2	float	linear_scale	Error	1	B635 Median	Cy5	
Circularity	integer	linear_scale	SpecializedQuantitationType				A measure of circularity from 0 to 100, using a metric based on the variance of the distance of each boundary pixel to the centroid of the feature: 100 is most circular, 0 is most non-circular. Circular features always have a circularity of 100, square fe
Dia.	integer	linear_scale	SpecializedQuantitationType				The diameter in um of the feature-indicator.
F Pixels	integer	linear_scale	SpecializedQuantitationType				The total number of feature pixels.
F532 % Sat.	integer	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels at wavelength 532 nm that are saturated.
F532 CV	integer	linear_scale	SpecializedQuantitationType			Cy3	The coefficient of variation of feature pixel intensity.
F532 Mean	integer	linear_scale	MeasuredSignal			Cy3	Mean feature pixel intensity at wavelength 532 nm.
F532 Mean - B532	integer	linear_scale	SpecializedQuantitationType			Cy3	The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.
F532 Median	integer	linear_scale	SpecializedQuantitationType			Cy3	Median feature pixel intensity at wavelength 532 nm.
F532 Median - B532	integer	linear_scale	SpecializedQuantitationType			Cy3	The median feature pixel intensity at wavelength 532 nm with the median background subtracted.
F532 SD	integer	linear_scale	Error		F532 Median	Cy3	The standard deviation of the feature intensity at wavelength 532 nm.
F532 Total Intensity	integer	linear_scale	SpecializedQuantitationType			Cy3	The sum of feature pixel intensities at 532 nm.
F563 % Sat.	integer	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels at wavelength 563 nm that are saturated.
F563 Mean	integer	linear_scale	MeasuredSignal			Cy3	Mean feature pixel intensity at wavelength 563 nm.
F563 Mean - B563	integer	linear_scale	SpecializedQuantitationType			Cy3	The mean feature pixel intensity at wavelength 563 nm with the median background subtracted.
F563 Median	integer	linear_scale	SpecializedQuantitationType			Cy3	Median feature pixel intensity at wavelength 563 nm.
F563 Median - B563	integer	linear_scale	SpecializedQuantitationType			Cy3	The median feature pixel intensity at wavelength 563 nm with the median background subtracted.
F563 SD	integer	linear_scale	Error		F563 Median	Cy3	The standard deviation of the feature intensity at wavelength 563 nm.
F635 % Sat.	integer	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels at wavelength 635 nm that are saturated.
F635 CV	integer	linear_scale	SpecializedQuantitationType			Cy5	The coefficient of variation of feature pixel intensity.
F635 Mean	integer	linear_scale	MeasuredSignal			Cy5	Mean feature pixel intensity at wavelength 635 nm.
F635 Mean - B635	integer	linear_scale	SpecializedQuantitationType			Cy5	The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.
F635 Median	integer	linear_scale	SpecializedQuantitationType			Cy5	Median feature pixel intensity at wavelength 635 nm.
F635 Median - B635	integer	linear_scale	SpecializedQuantitationType			Cy5	The median feature pixel intensity at wavelength 635 nm with the median background subtracted.
F635 SD	integer	linear_scale	Error		F635 Median	Cy5	The standard deviation of the feature intensity at wavelength 635 nm.
F635 Total Intensity	integer	linear_scale	SpecializedQuantitationType			Cy5	The sum of feature pixel intensities at 635 nm.
Flags	integer	linear_scale	SpecializedQuantitationType				The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.
Log Ratio	float	log_base_2	Ratio				Log (base 2) transform of the ratio of the medians.
Log Ratio (532/635)	float	log_base_2	Ratio				log (base 2) transform of the ratio of the medians.
Log Ratio (635/532)	float	log_base_2	Ratio				Log (base 2) transform of the ratio of the medians.
Mean of Ratios	float	linear_scale	SpecializedQuantitationType				The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios (532/635)	float	linear_scale	SpecializedQuantitationType				The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios (635/532)	float	linear_scale	SpecializedQuantitationType				The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Median of Ratios	float	linear_scale	SpecializedQuantitationType				The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Median of Ratios (532/635)	float	linear_scale	SpecializedQuantitationType				The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Median of Ratios (635/532)	float	linear_scale	SpecializedQuantitationType				The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Normalize	integer	unscaled	PresentAbsent				The normalization status of the feature (included/not included).
Ratio of Means	float	linear_scale	SpecializedQuantitationType				The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means (532/635)	float	linear_scale	SpecializedQuantitationType				The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means (635/532)	float	linear_scale	SpecializedQuantitationType				The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Medians	float	linear_scale	SpecializedQuantitationType				The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Medians (532/635)	float	linear_scale	SpecializedQuantitationType				The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Medians (635/532)	float	linear_scale	SpecializedQuantitationType				The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratios SD	float	linear_scale	Error		Median of Ratios		The geometric standard deviation of the pixel intensity ratios.
Ratios SD (532/635)	float	linear_scale	Error		Median of Ratios (532/635)		The geometric standard deviation of the pixel intensity ratios.
Ratios SD (635/532)	float	linear_scale	Error		Median of Ratios (635/532)		The geometric standard deviation of the pixel intensity ratios.
Rgn R  (532/635)	float	linear_scale	SpecializedQuantitationType				
Rgn R2	float	linear_scale	SpecializedQuantitationType				The coefficient of determination for the current regression value.
Rgn R2 (532/635)	float	linear_scale	SpecializedQuantitationType				The coefficient of determination for the current regression value.
Rgn R2 (635/532)	float	linear_scale	SpecializedQuantitationType				The coefficient of determination for the current regression value.
Rgn Ratio	float	linear_scale	SpecializedQuantitationType				The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn Ratio (532/635)	float	linear_scale	SpecializedQuantitationType				The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn Ratio (635/532)	float	linear_scale	SpecializedQuantitationType				The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R%G�%@	float	linear_scale	SpecializedQuantitationType				
Rgn R%G�%@ (635/532)	float	linear_scale	SpecializedQuantitationType				
Rgn R%G�%@ (532/635)	float	linear_scale	SpecializedQuantitationType				
SNR 532	float	linear_scale	SpecializedQuantitationType	1		Cy3	The signal-to-noise ratio at 532 nm, defined by (F532 Mean - B532 Mean) / (B532 SD)
SNR 635	float	linear_scale	SpecializedQuantitationType	1		Cy5	The signal-to-noise ratio at 635 nm, defined by (F635 Mean - B635 Mean) / (B635 SD)
Sum of Means	integer	linear_scale	SpecializedQuantitationType				The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Sum of Means (532/635)	integer	linear_scale	SpecializedQuantitationType				The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Sum of Means (635/532)	integer	linear_scale	SpecializedQuantitationType				The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Sum of Medians	integer	linear_scale	SpecializedQuantitationType				The sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Medians (532/635)	integer	linear_scale	SpecializedQuantitationType				The sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Medians (635/532)	integer	linear_scale	SpecializedQuantitationType				The sum of the median intensities for each wavelength, with the median background subtracted.
X	integer	linear_scale	SpecializedQuantitationType				The X-coordinate in um of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y	integer	linear_scale	SpecializedQuantitationType				The Y-coordinate in um of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
>>>GeneTAC							
Background med Cy3	float	linear_scale	MeasuredSignal	1		Cy3	
Background med Cy5	float	linear_scale	MeasuredSignal	1		Cy5	
Background med ratio	float	linear_scale	Ratio	1			
Background st dev Cy3	float	linear_scale	Error	1	Background med Cy3	Cy3	
Background st dev Cy5	float	linear_scale	Error	1	Background med Cy5	Cy5	
Signal med Cy3	float	linear_scale	MeasuredSignal			Cy3	
Signal med Cy5	float	linear_scale	MeasuredSignal			Cy5	
Signal med ratio	float	linear_scale	Ratio				
Signal st dev Cy3	float	linear_scale	Error		Signal med Cy3	Cy3	
Signal st dev Cy5	float	linear_scale	Error		Signal med Cy5	Cy5	
>>>ImaGene[BioDiscovery]							
Area To Perimeter_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	This quality measure defines the spot's circularity. Area of a spot is divided by a square of spot perimeter and multiplied by 4&#960;. As a result, this measure ranges from 0 (highly non-circular shape) to 1 (a perfect circle).
Area To Perimeter_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	This quality measure defines the spot's circularity. Area of a spot is divided by a square of spot perimeter and multiplied by 4&#960;. As a result, this measure ranges from 0 (highly non-circular shape) to 1 (a perfect circle).
Background Area_Cy3	integer	linear_scale	SpecializedQuantitationType	1		Cy3	Number of pixels in the local background region.
Background Area_Cy5	integer	linear_scale	SpecializedQuantitationType	1		Cy5	Number of pixels in the local background region.
Background Contamination Present_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Background Contamination Present_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Background Mean	float	linear_scale	MeasuredSignal	1			
Background Mean_Cy3	float	linear_scale	MeasuredSignal	1		Cy3	Pixel intensity averaged over the local background region.
Background Mean_Cy5	float	linear_scale	MeasuredSignal	1		Cy5	Pixel intensity averaged over the local background region.
Background Median_Cy3	float	linear_scale	SpecializedQuantitationType	1		Cy3	Median pixel intensity computed over the local background region.
Background Median_Cy5	float	linear_scale	SpecializedQuantitationType	1		Cy5	Median pixel intensity computed over the local background region.
Background Mode_Cy3	float	linear_scale	SpecializedQuantitationType	1		Cy3	Mode pixel intensity computed over the local background region.
Background Mode_Cy5	float	linear_scale	SpecializedQuantitationType	1		Cy5	Mode pixel intensity computed over the local background region.
Background Stdev	float	linear_scale	Error	1	Background Mean		
Background Stdev_Cy3	float	linear_scale	Error	1	Background Mean_Cy3	Cy3	Standard deviation of pixel intensities over the local background region.
Background Stdev_Cy5	float	linear_scale	Error	1	Background Mean_Cy5	Cy5	Standard deviation of pixel intensities over the local background region.
Background Total_Cy3	integer	linear_scale	SpecializedQuantitationType	1		Cy3	Total pixel intensity summed over the local background region.
Background Total_Cy5	integer	linear_scale	SpecializedQuantitationType	1		Cy5	Total pixel intensity summed over the local background region.
Background contamination present_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	0 if the spot passed background contamination test, 1 if it did not.
Background contamination present_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	0 if the spot passed background contamination test, 1 if it did not.
CM Offset-X_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	X offset (in pixels) of the spot's center of the mass from the expected position in the grid.
CM Offset-X_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	X offset (in pixels) of the spot's center of the mass from the expected position in the grid.
CM Offset-Y_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Y offset (in pixels) of the spot's center of the mass from the expected position in the grid.
CM Offset-Y_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Y offset (in pixels) of the spot's center of the mass from the expected position in the grid.
CM Offset_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Offset (in pixels) of the spot's center of the mass from the expected position in the grid.
CM Offset_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Offset (in pixels) of the spot's center of the mass from the expected position in the grid.
CM-X_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	X coordinate of the center of the mass of spot's signal region.
CM-X_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	X coordinate of the center of the mass of spot's signal region.
CM-Y_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Y coordinate of the center of the mass of spot's signal region.
CM-Y_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Y coordinate of the center of the mass of spot's signal region.
Control_Cy3	string_datatype	unscaled	SpecializedQuantitationType			Cy3	Name of a control type for current spot (no name means the spot is not a control spot).
Control_Cy5	string_datatype	unscaled	SpecializedQuantitationType			Cy5	Name of a control type for current spot (no name means the spot is not a control spot).
Diameter	integer	linear_scale	SpecializedQuantitationType				
Diameter_Cy3	integer	linear_scale	SpecializedQuantitationType			Cy3	Diameter (in pixels) of grid circle corresponding to the spot.
Diameter_Cy5	integer	linear_scale	SpecializedQuantitationType			Cy5	Diameter (in pixels) of grid circle corresponding to the spot.
Empty spot_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	0 if the spot passed offset test, 1 if it did not.
Empty spot_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	0 if the spot passed offset test, 1 if it did not.
Expected X_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	X coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column.
Expected X_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	X coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column.
Expected Y_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Y coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column.
Expected Y_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Y coordinate of expected position of the circle in the grid. Expected position in the grid is computed fitting least square lines to circle centers in every row and column.
Failed Control_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	0 if the control passed all tests, 1 if at least one of the tests failed.
Failed Control_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	0 if the control passed all tests, 1 if at least one of the tests failed.
Field	string_datatype	unscaled	SpecializedQuantitationType				Name of a field where the spot is located.
Flag	boolean	unscaled	PresentAbsent				
Flag_Cy3	integer	linear_scale	SpecializedQuantitationType			Cy3	Numeric code for the spot (0 - no flag, flag codes 1,...,7).
Flag_Cy5	integer	linear_scale	SpecializedQuantitationType			Cy5	Numeric code for the spot (0 - no flag, flag codes 1,...,7).
Gene ID	string_datatype	unscaled	SpecializedQuantitationType				Gene ID information for the spot.
Ignored % failed_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	0 if the spot passed ignored percentage test, 1 if it did not.
Ignored % failed_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	0 if the spot passed ignored percentage test, 1 if it did not.
Ignored Area_Cy3	integer	linear_scale	SpecializedQuantitationType			Cy3	Area of ignored regions directly neighboring ("touching") the signal area is computed.
Ignored Area_Cy5	integer	linear_scale	SpecializedQuantitationType			Cy5	Area of ignored regions directly neighboring ("touching") the signal area is computed.
Ignored Median_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Median pixel intensity computed over the local ignored region.
Ignored Median_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Median pixel intensity computed over the local ignored region.
Max Diam_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Diameter of the circle, the spot's signal region can be inscribed in.
Max Diam_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Diameter of the circle, the spot's signal region can be inscribed in.
Min Diam_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Diameter of the circle inscribed into the spot's signal region.
Min Diam_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Diameter of the circle inscribed into the spot's signal region.
Negative spot_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	1 if the spot was qualified as negative, 0 if it was not.
Negative spot_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	1 if the spot was qualified as negative, 0 if it was not.
Offset X_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	X Offset (in pixels) of the center of the grid circle from the expected position in the grid.
Offset X_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	X Offset (in pixels) of the center of the grid circle from the expected position in the grid.
Offset Y_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Y Offset (in pixels) of the center of the grid circle from the expected position in the grid.
Offset Y_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Y Offset (in pixels) of the center of the grid circle from the expected position in the grid.
Offset failed_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	0 if the spot passed offset test, 1 if it did not.
Offset failed_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	0 if the spot passed offset test, 1 if it did not.
Open Perimeter Failed_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Open Perimeter Failed_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Open Perimeter_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot.
Open Perimeter_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Computes the proportion of signal perimeter that touches the border of rectangular snip around the spot.
Open perimeter failed_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	0 if the spot open perimeter test, 1 if it did not.
Open perimeter failed_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	0 if the spot open perimeter test, 1 if it did not.
Perim-To-Area_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Perim-To-Area_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Perim-to-area failed_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	0 if the spot passed perimeter-to-area test, 1 if it did not.
Perim-to-area failed_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	0 if the spot passed perimeter-to-area test, 1 if it did not.
Position Offset_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	
Position Offset_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	
Position offset_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Offset (in pixels) of the center of the grid circle from the expected position in the grid.
Position offset_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Offset (in pixels) of the center of the grid circle from the expected position in the grid.
Saturated spot_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	1 if the spot was qualified as saturated, 0 if it was not.
Saturated spot_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	1 if the spot was qualified as saturated, 0 if it was not.
Selected spot_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	1 if the spot was selected in the software view at time of save, 0 if not.
Selected spot_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	1 if the spot was selected in the software view at time of save, 0 if not.
Shape Regularity	float	linear_scale	SpecializedQuantitationType				
Shape Regularity Failed_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Shape Regularity Failed_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Shape Regularity_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	The signal area of a spot is inscribed into a circle, then the number of non-signal pixels that fall within this circle is computed and divided by area of circle. This ratio is subtracted from 1 to give the Shape Regularity.
Shape Regularity_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	The signal area of a spot is inscribed into a circle, then the number of non-signal pixels that fall within this circle is computed and divided by area of circle. This ratio is subtracted from 1 to give the Shape Regularity.
Shape regularity failed_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	0 if the spot passed shape regularity test, 1 if it did not.
Shape regularity failed_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	0 if the spot passed shape regularity test, 1 if it did not.
Signal Area_Cy3	integer	linear_scale	SpecializedQuantitationType			Cy3	Number of pixels in the local signal region.
Signal Area_Cy5	integer	linear_scale	SpecializedQuantitationType			Cy5	Number of pixels in the local signal region.
Signal Contamination Present_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Signal Contamination Present_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Signal Mean	float	linear_scale	MeasuredSignal				
Signal Mean_Cy3	float	linear_scale	MeasuredSignal			Cy3	Pixel intensity averaged over the local signal region.
Signal Mean_Cy5	float	linear_scale	MeasuredSignal			Cy5	Pixel intensity averaged over the local signal region.
Signal Median_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Median pixel intensity computed over the local signal region.
Signal Median_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Median pixel intensity computed over the local signal region.
Signal Mode_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Mode pixel intensity computed over the local signal region (mode corresponds to the pick location in intensity distribution).
Signal Mode_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Mode pixel intensity computed over the local signal region (mode corresponds to the pick location in intensity distribution).
Signal Stdev	float	linear_scale	Error		Signal Mean		
Signal Stdev_Cy3	float	linear_scale	Error		Signal Mean_Cy3	Cy3	Standard deviation of pixel intensities over the local signal region.
Signal Stdev_Cy5	float	linear_scale	Error		Signal Mean_Cy5	Cy5	Standard deviation of pixel intensities over the local signal region.
Signal Total_Cy3	integer	linear_scale	SpecializedQuantitationType			Cy3	Total pixel intensity summed over the local signal region.
Signal Total_Cy5	integer	linear_scale	SpecializedQuantitationType			Cy5	Total pixel intensity summed over the local signal region.
Signal contamination present_Cy3	boolean	linear_scale	SpecializedQuantitationType			Cy3	0 if the spot passed signal contamination test, 1 if it did not.
Signal contamination present_Cy5	boolean	linear_scale	SpecializedQuantitationType			Cy5	0 if the spot passed signal contamination test, 1 if it did not.
Spot Area_Cy3	integer	linear_scale	SpecializedQuantitationType			Cy3	Signal Area plus Ignored Area.
Spot Area_Cy5	integer	linear_scale	SpecializedQuantitationType			Cy5	Signal Area plus Ignored Area.
XCoord	float	linear_scale	SpecializedQuantitationType				
XCoord_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	X coordinate (in pixels) of grid circle corresponding to the spot.
XCoord_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	X coordinate (in pixels) of grid circle corresponding to the spot.
YCoord	float	linear_scale	SpecializedQuantitationType				
YCoord_Cy3	float	linear_scale	SpecializedQuantitationType			Cy3	Y coordinate (in pixels) of grid circle corresponding to the spot.
YCoord_Cy5	float	linear_scale	SpecializedQuantitationType			Cy5	Y coordinate (in pixels) of grid circle corresponding to the spot.
>>>NimbleScan[NimbleGen Systems]							
GENE_EXPR_OPTION	string_datatype	unscaled	SpecializedQuantitationType				The CONTAINER name from the design file, if analysis was done by container or WHOLE_ARRAY if all replicate probe sets were combined into a single set. The default analysis is normally by container. CONTAINER names are generally named FORWARD/REVERSE/BLOCK
IMAGE_ID_CY3	string_datatype	unscaled	SpecializedQuantitationType			Cy3	The name of the image the data was extracted from, minus the .tif extension. For NimbleGen data sets, this will be the array identifier plus any additional information, like wavelength used to scan the array, or photomultiplier tube setting. The array ID
IMAGE_ID_CY5	string_datatype	unscaled	SpecializedQuantitationType			Cy5	The name of the image the data was extracted from, minus the .tif extension. For NimbleGen data sets, this will be the array identifier plus any additional information, like wavelength used to scan the array, or photomultiplier tube setting. The array ID
IMAGE_ID	string_datatype	unscaled	SpecializedQuantitationType				The name of the image the data was extracted from, minus the .tif extension. For NimbleGen data sets, this will be the array identifier plus any additional information, like wavelength used to scan the array, or photomultiplier tube setting. The array ID
MATCH_INDEX	integer	linear_scale	SpecializedQuantitationType				Integer number that ties probe pairs together. Using the combination of MATCH_INDEX and MISMATCH you can retrieve and distinguish the members of the probe pair. Required for expression arrays with mismatches. Must be unique for each probe pair of a given
MM_CY3	float	linear_scale	SpecializedQuantitationType			Cy3	The mismatch signal intensity for the probe pair. Will range from 0 to 65536. Will be zero for perfect match only designs.
MM_CY5	float	linear_scale	SpecializedQuantitationType			Cy5	The mismatch signal intensity for the probe pair. Will range from 0 to 65536. Will be zero for perfect match only designs.
PM_CY3	float	linear_scale	MeasuredSignal			Cy3	The perfect match signal intensity for the probe pair. Will range from 0 to 65536.
PM_CY5	float	linear_scale	MeasuredSignal			Cy5	The perfect match signal intensity for the probe pair. Will range from 0 to 65536.
MM	float	linear_scale	SpecializedQuantitationType				The mismatch signal intensity for the probe pair. Will range from 0 to 65536. Will be zero for perfect match only designs.
PM	float	linear_scale	MeasuredSignal				The perfect match signal intensity for the probe pair. Will range from 0 to 65536.
POSITION	integer	linear_scale	SpecializedQuantitationType				Position of the PROBE_SEQUENCE in the sequence/region of interest, starting from the left/5-prime end.
PROBE_ID	string_datatype	unscaled	SpecializedQuantitationType				The NimbleGen probe identifier. Used to identify a probe sequence within a design. Limited to 50 characters. For expression designs, a PROBE_ID is a 17 character string that looks like HSAP00P0001724033. The first four letters (HSAP) are the species code.
SEQ_ID	string_datatype	unscaled	SpecializedQuantitationType				The NimbleGen sequence identifier. Used to group the probe pairs together for determining gene expression summary values. Required - must be unique for each sequence/region of interest. Limited to 50 characters.
SEQ_URL	string_datatype	unscaled	SpecializedQuantitationType				When populated, URL to sequence information for the SEQ_ID.
>>>QuantArray[PerkinElmer]							
Cy3 Area	integer	linear_scale	SpecializedQuantitationType			Cy3	The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide.
Cy3 Area Filter	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Cy3 Background	float	linear_scale	MeasuredSignal	1		Cy3	Mean pixel Cy3 background intensity in Channel Cy3.
Cy3 Background Std Dev	float	linear_scale	Error	1	Cy3 Background	Cy3	Standard deviation of the raw Cy3 background pixel intensity.
Cy3 Background Subtr				1		Cy3	
Cy3 Bkg. Uniformity	float	linear_scale	SpecializedQuantitationType	1		Cy3	The uniformity of the pixels used in the background intensity calculation.
Cy3 Bkg. Uniformity Filter	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Cy3 Circularity	float	linear_scale	SpecializedQuantitationType			Cy3	Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray.
Cy3 Circularity Filter	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Cy3 Confidence	integer	linear_scale	SpecializedQuantitationType			Cy3	Unused QuantArray feature, will always = 1.
Cy3 Diameter	float	linear_scale	SpecializedQuantitationType			Cy3	Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide.
Cy3 Diameter Filter	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Cy3 Footprint	float	linear_scale	SpecializedQuantitationType			Cy3	The distance between the expected position of a spot and its actual measured position (in microns).
Cy3 Footprint Filter	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Cy3 Intensity	float	linear_scale	MeasuredSignal			Cy3	Mean pixel Cy3 foreground intensity in Channel Cy3.
Cy3 Intensity Std Dev	float	linear_scale	Error		Cy3 Intensity	Cy3	Standard deviation of the raw Cy3 foreground pixel intensity.
Cy3 Normalized & BackSubtr				1		Cy3	
Cy3 Normalized & BackSubtr Ratio				1		Cy3	
Cy3 Percent	float	linear_scale	SpecializedQuantitationType			Cy3	The portion of the overall spot fluorescence contributed by channel Cy3 (in percent).
Cy3 Ratio	float	linear_scale	SpecializedQuantitationType			Cy3	The portion of the overall spot fluorescence contributed by channel Cy3 (normalized so that channel Cy3 contribution equals 1).
Cy3 Replicate Filter	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Cy3 Signal Noise Ratio	float	linear_scale	Ratio	1		Cy3	The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews.
Cy3 Signal Noise Ratio Filter	float	linear_scale	SpecializedQuantitationType			Cy3	
Cy3 Spot Uniformity	float	linear_scale	SpecializedQuantitationType			Cy3	The uniformity of the pixels used in the spot foreground intensity calculation.This helps in determining the quality of the spot and aids in selecting the correct quantification output method.
Cy3 Spot Uniformity Filter	boolean	linear_scale	SpecializedQuantitationType			Cy3	
Cy5 Area	integer	linear_scale	SpecializedQuantitationType			Cy5	The area of the spot given as the number of pixels (in sq. microns). Used to determine whether the spot is close to the expected size or is an artifact on the slide.
Cy5 Area Filter	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Cy5 Background	float	linear_scale	MeasuredSignal	1		Cy5	Mean pixel Cy5 background intensity in Channel Cy5.
Cy5 Background Std Dev	float	linear_scale	Error	1	Cy5 Background	Cy5	Standard deviation of the raw Cy5 background pixel intensity.
Cy5 Background Subtr				1		Cy5	
Cy5 Bkg. Uniformity	float	linear_scale	SpecializedQuantitationType	1		Cy5	The uniformity of the pixels used in the background intensity calculation.
Cy5 Bkg. Uniformity Filter	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Cy5 Circularity	float	linear_scale	SpecializedQuantitationType			Cy5	Reports the degree to which a spot is close to a perfect circle. This measurement is used to determine the print quality of the microarray.
Cy5 Circularity Filter	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Cy5 Confidence	integer	linear_scale	SpecializedQuantitationType			Cy5	Unused QuantArray feature, will always = 1.
Cy5 Diameter	float	linear_scale	SpecializedQuantitationType			Cy5	Average diameter of the spot (in microns). Used to determine whether the spot is close to the expected size or is perhaps an artifact on the slide.
Cy5 Diameter Filter	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Cy5 Footprint	float	linear_scale	SpecializedQuantitationType			Cy5	The distance between the expected position of a spot and its actual measured position (in microns).
Cy5 Footprint Filter	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Cy5 Intensity	float	linear_scale	MeasuredSignal			Cy5	Mean pixel Cy5 foreground intensity in Channel Cy5.
Cy5 Intensity Std Dev	float	linear_scale	Error		Cy5 Intensity	Cy5	Standard deviation of the raw Cy5 foreground pixel intensity.
Cy5 Normalized & BackSubtr				1		Cy5	
Cy5 Normalized & BackSubtr Ratio				1		Cy5	
Cy5 Percent	float	linear_scale	SpecializedQuantitationType			Cy5	The portion of the overall spot fluorescence contributed by channel Cy5 (in percent).
Cy5 Ratio	float	linear_scale	SpecializedQuantitationType			Cy5	The portion of the overall spot fluorescence contributed by channel Cy5 (normalized so that channel Cy5 contribution equals 1).
Cy5 Replicate Filter	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Cy5 Signal Noise Ratio	float	linear_scale	Ratio	1		Cy5	The ratio of spot intensity to the standard deviation of the local background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews.
Cy5 Signal Noise Ratio Filter	float	linear_scale	SpecializedQuantitationType			Cy5	
Cy5 Spot Uniformity	float	linear_scale	SpecializedQuantitationType			Cy5	The uniformity of the pixels used in the spot foreground intensity calculation.This helps in determining the quality of the spot and aids in selecting the correct quantification output method.
Cy5 Spot Uniformity Filter	boolean	linear_scale	SpecializedQuantitationType			Cy5	
Ignore Filter	integer	linear_scale	SpecializedQuantitationType				Whether the feature quantitation is used in down-stream analysis (flagging feature as valid): 0 = feature invalid (null data); 1 = feature valid.
Number	integer	linear_scale	SpecializedQuantitationType				Unique integer for each spot.
X Location	integer	linear_scale	SpecializedQuantitationType				X pixel coordinate of spot center.
Y Location	integer	linear_scale	SpecializedQuantitationType				Y pixel coordinate of spot center.
log_normalised	float	log_base_2	Ratio				Ratio = log2 Cy5 - log2 Cy3, for dyeswap ratio *-1
normalised log(cy3/cy5) ratio	float	log	Ratio	0			
normalised log(cy5/cy3) ratio	float	log	Ratio	0			
Cy3 Background Mean	float	linear_scale	MeasuredSignal	1		Cy3	Mean pixel Cy3 background intensity in Channel Cy3.
Cy3 Background Median	integer	linear_scale	SpecializedQuantitationType	1		Cy3	Median pixel Cy3 background intensity in Channel Cy3.
Cy3 Background Mode	float	linear_scale	SpecializedQuantitationType	1		Cy3	Mode of pixel Cy3 background intensity in Channel Cy3.
Cy3 Background Total	integer	linear_scale	SpecializedQuantitationType	1		Cy3	Total pixel Cy3 background intensity in Channel Cy3.
Cy3 Flag	integer	unscaled	SpecializedQuantitationType			Cy3	
Cy3 Signal Mean	float	linear_scale	MeasuredSignal			Cy3	Mean pixel Cy3 foreground intensity in Channel Cy3.
Cy3 Signal Median	integer	linear_scale	SpecializedQuantitationType			Cy3	Median pixel Cy3 foreground intensity in Channel Cy3.
Cy3 Signal Mode	float	linear_scale	SpecializedQuantitationType			Cy3	Mode of pixel Cy3 foreground intensity in Channel Cy3.
Cy3 Signal Total	integer	linear_scale	SpecializedQuantitationType			Cy3	Total pixel Cy3 foreground intensity in Channel Cy3.
Cy5 Background Mean	float	linear_scale	MeasuredSignal	1		Cy5	Mean pixel Cy5 background intensity in Channel Cy5.
Cy5 Background Median	integer	linear_scale	SpecializedQuantitationType	1		Cy5	Median pixel Cy5 background intensity in Channel Cy5.
Cy5 Background Mode	float	linear_scale	SpecializedQuantitationType	1		Cy5	Mode of pixel Cy5 background intensity in Channel Cy5.
Cy5 Background Total	integer	linear_scale	SpecializedQuantitationType	1		Cy5	Total pixel Cy5 background intensity in Channel Cy5.
Cy5 Flag	integer	unscaled	SpecializedQuantitationType			Cy5	
Cy5 Signal Mean	float	linear_scale	MeasuredSignal			Cy5	Mean pixel Cy5 foreground intensity in Channel Cy5.
Cy5 Signal Median	integer	linear_scale	SpecializedQuantitationType			Cy5	Median pixel Cy5 foreground intensity in Channel Cy5.
Cy5 Signal Mode	float	linear_scale	SpecializedQuantitationType			Cy5	Mode of pixel Cy5 foreground intensity in Channel Cy5.
Cy5 Signal Total	integer	linear_scale	SpecializedQuantitationType			Cy5	Total pixel Cy5 foreground intensity in Channel Cy5.
>>>ScanAlyze[Stanford University]							
BGPIX	integer	linear_scale	SpecializedQuantitationType	1			Number of background pixels.
BOT	integer	linear_scale	SpecializedQuantitationType				Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).
CH1AB	float	linear_scale	SpecializedQuantitationType	1		Cy3	Mean intensities of background pixels of Cy3.
CH1B	float	linear_scale	MeasuredSignal	1		Cy3	Median intensities of background pixels of Cy3.
CH1EDGEA	float	linear_scale	SpecializedQuantitationType			Cy3	Mean magnitude of the horizontal & vertical Sobel edge vectors contained within each spot, for Cy3.
CH1GTB1	float	linear_scale	SpecializedQuantitationType			Cy3	Fraction of pixels in the spot greater than background (CH1B) of Cy3.
CH1GTB2	float	linear_scale	SpecializedQuantitationType			Cy3	Fraction of pixels in the spot greater than 1.5x the background (CH1B) for Cy3.
CH1I	float	linear_scale	MeasuredSignal			Cy3	Uncorrected Cy3 mean pixel intensity.
CH1KSD	float	linear_scale	SpecializedQuantitationType			Cy3	Value of Komogorov-Smirnov statistic that assesses the likelihood that the spot pixel intensity is drawn from the background distribution, for Cy3.
CH1KSP	float	linear_scale	SpecializedQuantitationType			Cy3	Probability value of Komogorov-Smirnov statistic that assesses the likelihood that the spot pixel intensity is drawn from the background distribution, for Cy3.
CH2AB	float	linear_scale	SpecializedQuantitationType	1		Cy5	Mean intensities of background pixels of Cy5.
CH2B	float	linear_scale	MeasuredSignal	1		Cy5	Median intensities of background pixels of Cy5.
CH2EDGEA	float	linear_scale	SpecializedQuantitationType			Cy5	Mean magnitude of the horizontal & vertical Sobel edge vectors contained within each spot, for Cy5.
CH2GTB1	float	linear_scale	SpecializedQuantitationType			Cy5	Fraction of pixels in the spot greater than background (CH2B) of Cy5.
CH2GTB2	float	linear_scale	SpecializedQuantitationType			Cy5	Fraction of pixels in the spot greater than 1.5x the background (CH2B) for Cy5.
CH2I	float	linear_scale	MeasuredSignal			Cy5	Uncorrected Cy5 mean pixel intensity.
CH2KSD	float	linear_scale	SpecializedQuantitationType			Cy5	Value of Komogorov-Smirnov statistic that assesses the likelihood that the spot pixel intensity is drawn from the background distribution, for Cy5.
CH2KSP	float	linear_scale	SpecializedQuantitationType			Cy5	Probability value of Komogorov-Smirnov statistic that assesses the likelihood that the spot pixel intensity is drawn from the background distribution, for Cy5.
COL	integer	linear_scale	SpecializedQuantitationType				The column within the grid that the spot is contained.
CORR	float	linear_scale	SpecializedQuantitationType				The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.
EDGE	integer	unscaled	SpecializedQuantitationType				
FLAG	integer	unscaled	Failed				User defined spot flag (default 0).
GRID	integer	linear_scale	SpecializedQuantitationType				The grid in which the spot is contained.
LEFT	integer	linear_scale	SpecializedQuantitationType				Box left: int(((centerY - radius) - yoffset) / pixelSize).
LFRAT	float	linear_scale	SpecializedQuantitationType				When single pixel intensities on channel 1 (Cy3) are plotted against those in channel 2 (Cy5) they fall on a straight line with a slope equal to the ratio. The least-squares fit of a line to the points, minimizing the sum of the squares shortest distance
MRAT	float	linear_scale	SpecializedQuantitationType				Contains median of Ch2PI-CH2B/Ch1PI-CH1B where Ch1PI & Ch2PI represent single pixel intensities.
RAT2	float	linear_scale	Ratio				Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 2/Channel 1 ratio, (CH2I - CH2B)/(CH1 - CH1B) or Red/Green ratio.
REGR	float	linear_scale	SpecializedQuantitationType				When single pixel intensities on channel 1 (Cy3) are plotted against those in channel 2 (Cy5) they fall on a straight line with a slope equal to the ratio. This represents the linear regression of Cy5 on Cy3.
RIGHT	integer	linear_scale	SpecializedQuantitationType				Box right: int(((centerY + radius) - yoffset) / pixelSize).
SPIX	integer	linear_scale	SpecializedQuantitationType				Count of the number of pixels in the spot.
SPOT	integer	linear_scale	SpecializedQuantitationType				Unique index of spot in file - counting starts with grid1, moves along row1 from column1 until the last column, then advances to the next row; after all rows in grid1 are assigned an index, counting proceeds to grid2, etc...
TOP	integer	linear_scale	SpecializedQuantitationType				Box top: int(((centerX - radius) - Xoffset) / pixelSize).
>>>ScanArray Express[PerkinElmer]							
% > B543+1SD	float	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, in the 543nm channel.
% > B543+2SD	float	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, in the 543nm channel.
% > B633+1SD	float	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, in the 633nm channel.
% > B633+2SD	float	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, in the 633nm channel.
B Pixels	integer	linear_scale	SpecializedQuantitationType				The total number of background pixels.
B543 Mean	float	linear_scale	MeasuredSignal	1		Cy3	Mean pixel background intensity in 543nm channel.
B543 Median	float	linear_scale	SpecializedQuantitationType	1		Cy3	Median pixel background intensity in 543nm channel.
B543 SD	float	linear_scale	Error	1	B543 Median	Cy3	Standard deviation of the raw 543nm background pixel intensity.
B633 Mean	float	linear_scale	MeasuredSignal	1		Cy5	Mean pixel background intensity in 633nm channel.
B633 Median	float	linear_scale	SpecializedQuantitationType	1		Cy5	Median pixel background intensity in 633nm channel.
B633 SD	float	linear_scale	Error	1	B633 Median	Cy5	Standard deviation of the raw 633nm background pixel intensity.
Cy3 % > B + 1 SD	float	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, in the Cy3 channel.
Cy3 % > B + 2 SD	float	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, in the Cy3 channel.
Cy3 B Mean	float	linear_scale	MeasuredSignal	1		Cy3	Mean pixel Cy3 background intensity in Channel Cy3.
Cy3 B Median	float	linear_scale	SpecializedQuantitationType	1		Cy3	Median pixel Cy3 background intensity in Channel Cy3.
Cy3 B SD	float	linear_scale	Error	1	Cy3 B Median	Cy3	Standard deviation of the raw Cy3 background pixel intensity.
Cy3 F % Sat.	float	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels in the Cy3 channel that are saturated.
Cy3 Log Ratio							
Cy3 Mean	float	linear_scale	MeasuredSignal			Cy3	Mean pixel Cy3 foreground intensity in Channel Cy3.
Cy3 Mean - B	float	linear_scale	SpecializedQuantitationType			Cy3	The mean feature pixel intensity in the Cy3 channel with the mean background subtracted.
Cy3 Mean of Ratios							
Cy3 Median	float	linear_scale	SpecializedQuantitationType			Cy3	Median pixel Cy3 foreground intensity in Channel Cy3.
Cy3 Median - B	float	linear_scale	SpecializedQuantitationType			Cy3	The median feature pixel intensity in the Cy3 channel with the median background subtracted.
Cy3 Median of Ratios							
Cy3 N (Mean-B)	float	linear_scale	DerivedSignal			Cy3	Mean pixel Cy3 foreground intensity in Channel Cy3 with the mean background subtracted, globally normalized.
Cy3 N (Median-B)	float	linear_scale	SpecializedQuantitationType			Cy3	Median pixel Cy3 foreground intensity in Channel Cy3 with the median background subtracted, globally normalized.
Cy3 N Log Ratio							
Cy3 N Mean	float	linear_scale	DerivedSignal			Cy3	Globally normalized mean pixel Cy3 foreground intensity in Channel Cy3.
Cy3 N Mean of Ratios							
Cy3 N Median	float	linear_scale	SpecializedQuantitationType			Cy3	Globally normalized median pixel Cy3 foreground intensity in Channel Cy3.
Cy3 N Median of Ratios							
Cy3 N Ratio of Means							
Cy3 N Ratio of Medians							
Cy3 N Rgn Ratio							
Cy3 Ratio of Means							
Cy3 Ratio of Medians							
Cy3 Ratios SD							
Cy3 Rgn Ratio							
Cy3 Rgn R%G�%@							
Cy3 SD	float	linear_scale	Error		Cy3 Median	Cy3	Standard deviation of the raw Cy3 foreground pixel intensity.
Cy3 SignalNoiseRatio	float	linear_scale	Ratio			Cy3	The ratio of spot Cy3 intensity to the standard deviation of the local Cy3 background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews.
Cy5 % > B + 1 SD	float	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, in the Cy5 channel.
Cy5 % > B + 2 SD	float	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, in the Cy5 channel.
Cy5 B Mean	float	linear_scale	MeasuredSignal	1		Cy5	Mean pixel Cy5 background intensity in Channel Cy5.
Cy5 B Median	float	linear_scale	SpecializedQuantitationType	1		Cy5	Median pixel Cy5 background intensity in Channel Cy5.
Cy5 B SD	float	linear_scale	Error	1	Cy5 B Median	Cy5	Standard deviation of the raw Cy5 background pixel intensity.
Cy5 F % Sat.	float	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels in the Cy5 channel that are saturated.
Cy5 Log Ratio							
Cy5 Mean	float	linear_scale	MeasuredSignal			Cy5	Mean pixel Cy5 foreground intensity in Channel Cy5.
Cy5 Mean - B	float	linear_scale	SpecializedQuantitationType			Cy5	The mean feature pixel intensity in the Cy5 channel with the mean background subtracted.
Cy5 Mean of Ratios							
Cy5 Median	float	linear_scale	SpecializedQuantitationType			Cy5	Median pixel Cy5 foreground intensity in Channel Cy5.
Cy5 Median - B	float	linear_scale	SpecializedQuantitationType			Cy5	The median feature pixel intensity in the Cy5 channel with the median background subtracted.
Cy5 Median of Ratios							
Cy5 N (Mean-B)	float	linear_scale	DerivedSignal			Cy5	Mean pixel Cy5 foreground intensity in Channel Cy5 with the mean background subtracted, globally normalized.
Cy5 N (Median-B)	float	linear_scale	SpecializedQuantitationType			Cy5	Median pixel Cy5 foreground intensity in Channel Cy5 with the median background subtracted, globally normalized.
Cy5 N Log Ratio							
Cy5 N Mean	float	linear_scale	DerivedSignal			Cy5	Globally normalized mean pixel Cy5 foreground intensity in Channel Cy5.
Cy5 N Mean of Ratios							
Cy5 N Median	float	linear_scale	SpecializedQuantitationType			Cy5	Globally normalized median pixel Cy5 foreground intensity in Channel Cy5.
Cy5 N Median of Ratios							
Cy5 N Ratio of Means							
Cy5 N Ratio of Medians							
Cy5 N Rgn Ratio							
Cy5 Ratio of Means							
Cy5 Ratio of Medians							
Cy5 Ratios SD							
Cy5 Rgn Ratio							
Cy5 Rgn R%G�%@							
Cy5 SD	float	linear_scale	Error		Cy5 Median	Cy5	Standard deviation of the raw Cy5 foreground pixel intensity.
Cy5 SignalNoiseRatio	float	linear_scale	Ratio			Cy5	The ratio of spot Cy5 intensity to the standard deviation of the local Cy5 background of all spots in the microarray. Spots with a low Signal/Noise Ratio can be quickly identified for later reviews.
Dia.	integer	linear_scale	SpecializedQuantitationType				The diameter in um of the feature-indicator.
Diameter	integer	linear_scale	SpecializedQuantitationType				The diameter in um of the feature-indicator.
F Pixels	integer	linear_scale	SpecializedQuantitationType				The total number of feature pixels.
F543 % Sat.	float	linear_scale	SpecializedQuantitationType			Cy3	The percentage of feature pixels in the 543nm channel that are saturated.
F543 Mean	float	linear_scale	MeasuredSignal			Cy3	Mean pixel foreground intensity in 543nm channel.
F543 Mean - B543	float	linear_scale	SpecializedQuantitationType			Cy3	The mean feature pixel intensity in the 543nm channel with the mean background subtracted.
F543 Median	float	linear_scale	SpecializedQuantitationType			Cy3	Median pixel foreground intensity in 543nm channel.
F543 Median - B543	float	linear_scale	SpecializedQuantitationType			Cy3	The median feature pixel intensity in the 543nm channel with the median background subtracted.
F543 SD	float	linear_scale	Error		F543 Median	Cy3	Standard deviation of the raw 543nm foreground pixel intensity.
F633 % Sat.	float	linear_scale	SpecializedQuantitationType			Cy5	The percentage of feature pixels in the 633nm channel that are saturated.
F633 Mean	float	linear_scale	MeasuredSignal			Cy5	Mean pixel foreground intensity in 633nm channel.
F633 Mean - B633	float	linear_scale	SpecializedQuantitationType			Cy5	The mean feature pixel intensity in the 633nm channel with the mean background subtracted.
F633 Median	float	linear_scale	SpecializedQuantitationType			Cy5	Median pixel foreground intensity in 633nm channel.
F633 Median - B633	float	linear_scale	SpecializedQuantitationType			Cy5	The median feature pixel intensity in the 633nm channel with the median background subtracted.
F633 SD	float	linear_scale	Error		F633 Median	Cy5	Standard deviation of the raw 633nm foreground pixel intensity.
Flags	integer	unscaled	SpecializedQuantitationType				
Footprint	integer	linear_scale	SpecializedQuantitationType				
ID	string_datatype	unscaled	SpecializedQuantitationType				
Index	integer	linear_scale	SpecializedQuantitationType				
Log Ratio	float	log_base_2	Ratio				
Log Ratio (633/543)	float	log_base_2	Ratio				
Mean of Ratios	float	linear_scale	SpecializedQuantitationType				The mean of pixel-by-pixel ratios of pixel intensities.
Mean of Ratios (633/543)	float	linear_scale	SpecializedQuantitationType				The mean of pixel-by-pixel ratios of pixel intensities.
Median of Ratios	float	linear_scale	SpecializedQuantitationType				The median of pixel-by-pixel ratios of pixel intensities.
Median of Ratios (633/543)	float	linear_scale	SpecializedQuantitationType				The median of pixel-by-pixel ratios of pixel intensities.
N Log Ratio	float	linear_scale	SpecializedQuantitationType				
N Mean of Ratios	float	linear_scale	SpecializedQuantitationType				
N Median of Ratios	float	linear_scale	SpecializedQuantitationType				
N Ratio of Means	float	linear_scale	SpecializedQuantitationType				
N Ratio of Medians	float	linear_scale	SpecializedQuantitationType				
N Rgn Ratio	float	linear_scale	SpecializedQuantitationType				
Name	string_datatype	unscaled	SpecializedQuantitationType				
Normalize	integer	unscaled	PresentAbsent				The normalization status of the feature (included/not included).
Ratio of Means	float	linear_scale	SpecializedQuantitationType				The ratio of the mean intensities of each feature for each wavelength.
Ratio of Means (633/543)	float	linear_scale	SpecializedQuantitationType				The ratio of the mean intensities of each feature for each wavelength.
Ratio of Medians	float	linear_scale	SpecializedQuantitationType				The ratio of the median intensities of each feature for each wavelength.
Ratio of Medians (633/543)	float	linear_scale	SpecializedQuantitationType				The ratio of the median intensities of each feature for each wavelength.
Ratios SD	float	linear_scale	SpecializedQuantitationType		Median of Ratios		
Ratios SD (633/543)	float	linear_scale	SpecializedQuantitationType		Median of Ratios (633/543)		
Rgn R2	float	linear_scale	SpecializedQuantitationType				
Rgn R2 (633/543)	float	linear_scale	SpecializedQuantitationType				
Rgn Ratio	float	linear_scale	SpecializedQuantitationType				
Rgn Ratio (633/543)	float	linear_scale	SpecializedQuantitationType				
Rgn R%G�%@ (633/543)	float	linear_scale	SpecializedQuantitationType				
Sum of Means	float	linear_scale	SpecializedQuantitationType				The sum of the mean intensities for each wavelength.
Sum of Medians	float	linear_scale	SpecializedQuantitationType				The sum of the median intensities for each wavelength.
X	integer	linear_scale	SpecializedQuantitationType				X coordinate of spot center.
Y	integer	linear_scale	SpecializedQuantitationType				Y coordinate of spot center.
>>>SpotFinder[TIGR]							
BGA	integer	linear_scale	MeasuredSignal	1		Cy3	Spot background in Cy3 channel.
BGB	integer	linear_scale	MeasuredSignal	1		Cy5	Spot background in Cy5 channel.
BkgA	integer	linear_scale	MeasuredSignal	1		Cy3	Spot background in Cy3 channel.
BkgB	integer	linear_scale	MeasuredSignal	1		Cy5	Spot background in Cy5 channel.
Flag	string_datatype	unscaled	SpecializedQuantitationType				Flag values are generated based on next conditions: A - the number of non-saturated pixels in spot is 0; B- number of non-saturated pixels in spot is between 30 and 50; C- number of non saturated pixels in spot is more then 50; S- fully or partially satur
Flag A	string_datatype	unscaled	SpecializedQuantitationType			Cy3	Spot flag in channel A. This flag is set by QC filter.
Flag B	string_datatype	unscaled	SpecializedQuantitationType			Cy5	Spot flag in channel B. This flag is set by QC filter.
FlagA	string_datatype	unscaled	SpecializedQuantitationType			Cy3	Spot flag in channel A. This flag is set by QC filter.
FlagB	string_datatype	unscaled	SpecializedQuantitationType			Cy5	Spot flag in channel B. This flag is set by QC filter.
IA	integer	linear_scale	MeasuredSignal			Cy3	Spot intensity in Cy3 channel corrected for background.
IB	integer	linear_scale	MeasuredSignal			Cy5	Spot intensity in Cy5 channel corrected for background.
MNA	integer	linear_scale	SpecializedQuantitationType			Cy3	Mean intensity value in Cy3 channel.
MNB	integer	linear_scale	SpecializedQuantitationType			Cy5	Mean intensity value in Cy5 channel.
MeanR	float	linear_scale	Ratio				Spot mean ratio
MedA	integer	linear_scale	SpecializedQuantitationType			Cy3	Median intensity in Cy3 channel.
MedB	integer	linear_scale	SpecializedQuantitationType			Cy5	Median intensity in Cy5 channel.
MedBkgA	integer	linear_scale	SpecializedQuantitationType			Cy3	Median background intensity in Cy3 channel.
MedBkgB	integer	linear_scale	SpecializedQuantitationType			Cy5	Median background intensity in Cy5 channel.
MedianR	float	linear_scale	Ratio				Spot median ratio.
ModeR	float	linear_scale	Ratio				Spot mode ratio.
PValueA	float	linear_scale	SpecializedQuantitationType			Cy3	P-value in Cy3 channel.
PValueB	float	linear_scale	SpecializedQuantitationType			Cy5	P-value in Cy5 channel.
QC	float	linear_scale	SpecializedQuantitationType				Spot total QC score. This is a mean of QC scores in Cy3 and Cy5 channels.
QCA	float	linear_scale	SpecializedQuantitationType			Cy3	Spot QC score in channel A. This is a geometric mean of shape and S/N QC scores in channel A. S/N QC score is calculated as percentage of pixels in a spot with values higher than 2*median(local BKG). Spot shape QC score is defined as ratio of spot area to
QCB	float	linear_scale	SpecializedQuantitationType			Cy5	Spot QC score in channel B. This is a geometric mean of shape and S/N QC scores in channel B. S/N QC score is calculated as percentage of pixels in a spot with values higher than 2*median(local BKG). Spot shape QC score is defined as ratio of spot area to
QCscore	float	linear_scale	SpecializedQuantitationType				
SA	integer	linear_scale	SpecializedQuantitationType				Spot total area in pixels.
SC	integer	unscaled	SpecializedQuantitationType				
SDA	float	linear_scale	Error		IA	Cy3	Standard deviation for spot pixels in Cy3 channel.
SDB	float	linear_scale	Error		IB	Cy5	Standard deviation for spot pixels in Cy5 channel.
SDBkgA	float	linear_scale	Error	1	BkgA	Cy3	Standard deviation of the background value in Cy3 channel.
SDBkgB	float	linear_scale	Error	1	BkgB	Cy5	Standard deviation of the background value in Cy5 channel.
SF	float	linear_scale	SpecializedQuantitationType				
SR	integer	unscaled	SpecializedQuantitationType				
Sat	float	linear_scale	SpecializedQuantitationType				Spot saturation factor. This measure shows the percentage of non-saturated pixels in the spot used for integration.
UID	integer	linear_scale	SpecializedQuantitationType				Unique identifier for this spot.
>>>UCSF Spot							
Dapi	float	linear_scale	MeasuredSignal			DAPI	
DapiBack	float	linear_scale	MeasuredSignal	1		DAPI	
DapiFore	float	linear_scale	SpecializedQuantitationType			DAPI	
Flag	integer	linear_scale	Failed				
Log2MedRat	float	log_base_2	Ratio				
Log2Rat	float	log_base_2	Ratio				
Log2Slope	float	log_base_2	SpecializedQuantitationType				
MeanLog2Rat	float	log_base_2	SpecializedQuantitationType				
MeanRat	float	linear_scale	SpecializedQuantitationType				
MedianRatio	float		Ratio				
MinF-B	float		SpecializedQuantitationType				
OriginDist	float		SpecializedQuantitationType				
RawRat	float	linear_scale	Ratio				
Ref	float	linear_scale	MeasuredSignal				
RefBack	float	linear_scale	MeasuredSignal	1			
RefBackSD		linear_scale	Error	1	RefBack		
RefFore	float	linear_scale	SpecializedQuantitationType				
RefForeSD		linear_scale	Error		RefFore		
RefIntercept	float		SpecializedQuantitationType				
RefZstat			PValue				
Slope	float	linear_scale	SpecializedQuantitationType				
SpotCorr	float		DerivedSignal				
Test	float	linear_scale	MeasuredSignal	1			
TestBack	float	linear_scale	MeasuredSignal	1			
TestBackSD		linear_scale	Error	1	TestBack		
TestFore	float	linear_scale	SpecializedQuantitationType				
TestForeSD		linear_scale	Error		TestFore		
TestIntercept	float		SpecializedQuantitationType				
TestZstat			PValue				
nback	integer	linear_scale	SpecializedQuantitationType	1			
nfore	integer	linear_scale	SpecializedQuantitationType				
>>>Uni of Toronto in-house analysis software							
B532 Location	float	linear_scale	MeasuredSignal	1		Cy3	
B635 Location	float	linear_scale	MeasuredSignal	1		Cy5	
F532 Location	float	linear_scale	MeasuredSignal			Cy3	
F635 Location	float	linear_scale	MeasuredSignal			Cy5	
Intensity	float	log_base_10	SpecializedQuantitationType				
Raw Log Ratio	float	log_base_10	Ratio	1			
