read.AgilentFE {Agi4x44PreProcess} | R Documentation

## Read Agilent Feature Extraction *.txt data files

### Description

Read the data files generated by the Agilent Feature Extraction image analysis software

### Usage

            read.AgilentFE(targets, makePLOT)

### Arguments

`targets` | A data frame that specifies experimental conditions under which each sample has been obtained.
`makePLOT` | logical, if `TRUE` the function display boxplots and density plots of foreground 'ProcessedSignal' and 'MeanSignal' and background 'BGMedianSignal' and 'BGUsed'

### Details

The function reads the *.txt files generated by the AFE Software using the 'read.maimages' function of 'limma' package.

Data, colected with the Agilent Feature Extraction Software, are stored in a RGList object with the following components:

dd$R: | 'gProcessedSignal'
dd$G: | 'gMeanSignal'
dd$Rb: | 'gBGMedianSignal'
dd$Gb: | 'gBGUsed'
dd$targets: | 'targets'
dd$genes$ProbeName: | 'Probe Name'
dd$genes$GeneName: | 'Gene Name'
dd$genes$SystematicName: | 'Systematic Name'
dd$genes$Description: | 'Description Name'
dd$genes$Sequence: | '60 bases Sequence'
dd$genes$ControlType: | 'FLAG to specify the sort of feature'
dd$other$gIsWellAboveBG: | 'FLAG IsWellAboveBG'
dd$other$gIsFound: | 'FLAG IsFound'
dd$other$gIsSaturated: | 'FLAG IsSaturated'
dd$other$gIsFeatPopnOL: | 'FLAG IsFeatPopnOL'
dd$other$gIsFeatNonUnifOL: | 'FLAG IsFeatNonUnifOL'
dd$other$chr_coord: | 'CHR coordinate (from Agilent data files)

'MeanSignal' is the spot Raw mean signal. 'ProcessedSignal' is the signal processed by the AFE software analysis software (AFE). It contains the Multiplicatively Detrend Bacground Substracted Signal if detrending option is selected and it helps. If the detrending does not help, the 'ProcessedSignal' will be the Bacground Subtracted Signal. 'BGMedianSignal' is the Median local background signal. 'BGUsed' depends on the AFE settings for the type of background method and the setting for the spatial detrend. Usually, the Background Signal Used is the sum of the local bacground + the spatial detrending surface value computed by the AFE software. To view the values used to calculate this variable using different bakground signals and settings of spatial detrend and global background adjust, see Table 33 on page 213 in the AFE reference guide.

Later, if a BioC annotation package is provided, 'SystematicName', 'GeneName' and 'Description' fields are replaced, respectively, by the corresponding ACCNUM, SYMBOL and DESCRIPTION obtained from the annotation package.

### Value

An RGList containing:

`RGList$Rf` | matrix, 'gProcessedSignal'
`RGList$Gf` | matrix, 'gMeanSignal'
`RGList$Rb` | matrix, 'gBGMedianSignal'
`RGList$Gb` | matrix, 'gBGUsed'
`RGList$targets` | data.frame, 'FileName'
`RGList$genes$ProbeName` | character, 'AGilent Probe Name'
`RGList$genes$GeneName` | character, 'Symbol Gene Name'
`RGList$genes$SystematicName` | character, 'Systematic Gene Name'
`RGList$genes$Description` | character, 'Gene Description'
`RGList$genes$Sequence` | character, 'Sequence of the 60 mer probe'
`RGList$genes$ControlType` | integer, '0'= Feature, '1'= Positive control, '-1'= Negative control
`RGList$other$gIsWellAboveBG` | matrix, FLAG to classify signal if 'IsWellAboveBG=1' or 'not=0'
`RGList$other$gIsFound` | matrix, FLAG to classify signal if 'IsFound=1' or 'not=0'
`RGList$other$gIsSaturated` | matrix, FLAG to classify signal if 'IsSaturated = 1' or 'not=0'
`RGList$other$gIsFeatPopnOL` | matrix, FLAG to classify signal if 'IsFeatPopnOL = 0' or 'not=1'
`RGList$other$gIsFeatNonUnifOL` | matrix, FLAG to classify signal if 'gIsFeatNonUnifOL = 0' or 'not=1'
`RGList$other$chr_coord` | matrix, chr coordinates for the 60 mer Agilent probe

### Author(s)

Pedro Lopez-Romero

### References

Agilent Feature Extraction Reference Guide http://www.Agilent.com

### See Also

`read.targets` `dd` `targets`

### Examples

    ## Not run:
            dd=read.AgilentFE(targets,makePLOT=TRUE)
    ## End(Not run)
            data(dd)

[Package Agi4x44PreProcess version 1.4.0 Index]