Entry: BLData
Aliases: BLData
Keywords: datasets
Description: BeadLevelList for the example experiment
URL: ../../../library/beadarray/html/BLData.html

Entry: BSData
Aliases: BSData
Keywords: datasets
Description: BeadSummaryList for the example experiment
URL: ../../../library/beadarray/html/BSData.html

Entry: BeadLevelList-class
Aliases: BeadLevelList-class coerce,BeadLevelList,exprSet2-method
Keywords: classes data
Description: Red, Green Intensity List - class
URL: ../../../library/beadarray/html/BeadLevelList.html

Entry: BeadSummaryList-class
Aliases: BeadSummaryList-class
Keywords: classes data
Description: Stores bead summary data - class
URL: ../../../library/beadarray/html/BeadSummaryList.html

Entry: LargeDataObject-class
Aliases: LargeDataObject-class show,LargeDataObject-method
Keywords: classes data
Description: Large Data Object - class
URL: ../../../library/beadarray/html/LargeDataObject.html

Entry: backgroundCorrectBeads
Aliases: backgroundCorrectBeads
Keywords: methods
Description: Background Correct a BeadLevelList object
URL: ../../../library/beadarray/html/backgroundCorrectBeads.html

Entry: biotin_controls
Aliases: biotin_controls
Keywords: datasets
Description: ProbeIDs of Biotin controls
URL: ../../../library/beadarray/html/biotin_controls.html

Entry: cbind
Aliases: cbind.BeadLevelList cbind.BeadSummaryList rbind.BeadSummaryList
Keywords: manip
Description: Combine BeadLevelList or BeadSummaryList Objects
URL: ../../../library/beadarray/html/cbind.html

Entry: checkRandomness
Aliases: checkRandomness chitest
Keywords: methods
Description: Test for random distribution of co-ordinates
URL: ../../../library/beadarray/html/checkRandomness.html

Entry: createBeadSummaryData
Aliases: createBeadSummaryData
Keywords: methods
Description: Produce bead averages
URL: ../../../library/beadarray/html/createBeadSummaryData.html

Entry: cy3_controls
Aliases: cy3_controls
Keywords: datasets
Description: ProbeIDs of cy3 controls
URL: ../../../library/beadarray/html/cy3_controls.html

Entry: dim
Aliases: dim.BeadLevelList dim.BeadSummaryList length.BeadLevelList length.BeadSummaryList
Keywords: array
Description: Retrieve the Dimensions of an BeadLevelList or BeadSummaryList
URL: ../../../library/beadarray/html/dim.html

Entry: dimnames
Aliases: dimnames.BeadLevelList dimnames.BeadSummaryList
Keywords: array
Description: Retrieve the Dimension Names of an BeadLevelList or BeadSummaryList Object
URL: ../../../library/beadarray/html/dimnames.html

Entry: displayTIFFImage
Aliases: displayTIFFImage showTIFF FindIlluminaSpotl Recenter IdentifyIntensity IdentifyBeads
Keywords: hplot
Description: Display part of a TIFF Image
URL: ../../../library/beadarray/html/displayTIFFImage.html

Entry: findAllOutliers
Aliases: findAllOutliers
Keywords: methods
Description: Find outliers on array
URL: ../../../library/beadarray/html/findAllOutliers.html

Entry: findBeadStatus
Aliases: findBeadStatus getProbeIndices getProbeIndicesC
Keywords: methods
Description: Find Outliers
URL: ../../../library/beadarray/html/findBeadStatus.html

Entry: findHighestChis
Aliases: findHighestChis
Keywords: methods
Description: Find least randomly distributed beads
URL: ../../../library/beadarray/html/findHighestChis.html

Entry: findHighestSD
Aliases: findHighestSD
Keywords: methods
Description: Highest standard deviation.
URL: ../../../library/beadarray/html/findHighestSD.html

Entry: findLowestCounts
Aliases: findLowestCounts
Keywords: methods
Description: Find Lowest bead counts
URL: ../../../library/beadarray/html/findLowestCounts.html

Entry: findMostOutliers
Aliases: findMostOutliers
Keywords: methods
Description: Beads with most outliers
URL: ../../../library/beadarray/html/findMostOutliers.html

Entry: getDimensions
Aliases: getDimensions
Keywords: methods
Description: Get dimension of an array
URL: ../../../library/beadarray/html/getDimensions.html

Entry: getMeanIntensities
Aliases: getMeanIntensities
Keywords: methods
Description: Find Bead Type Averages
URL: ../../../library/beadarray/html/getMeanIntensities.html

Entry: getProbeCoords
Aliases: getProbeCoords
Keywords: methods
Description: Find Bead Co-ordinates
URL: ../../../library/beadarray/html/getProbeCoords.html

Entry: getProbeIDs
Aliases: getProbeIDs
Keywords: methods
Description: Get unique ProbeIDs
URL: ../../../library/beadarray/html/getProbeIDs.html

Entry: getProbeInfo
Aliases: getProbeInfo
Keywords: methods
Description: Get information for ProbeID
URL: ../../../library/beadarray/html/getProbeInfo.html

Entry: getProbeIntensities
Aliases: getProbeIntensities
Keywords: methods
Description: Get Intensites of Beads
URL: ../../../library/beadarray/html/getProbeIntensities.html

Entry: getUnregisteredBeads
Aliases: getUnregisteredBeads
Keywords: methods
Description: Finds unregistered beads
URL: ../../../library/beadarray/html/getUnregisteredBeads.html

Entry: histBeadCounts
Aliases: histBeadCounts
Keywords: hplot
Description: Plot numbers of each bead
URL: ../../../library/beadarray/html/histBeadCounts.html

Entry: housekeeping_controls
Aliases: housekeeping_controls
Keywords: datasets
Description: ProbeIDs of housekeeping controls
URL: ../../../library/beadarray/html/housekeeping_controls.html

Entry: hs_controls
Aliases: hs_controls
Keywords: datasets
Description: ProbeIDs of high stringency controls
URL: ../../../library/beadarray/html/hs_controls.html

Entry: labelling_controls
Aliases: labelling_controls
Keywords: datasets
Description: ProbeIDs of housekeeping controls
URL: ../../../library/beadarray/html/labelling_controls.html

Entry: ls_controls
Aliases: ls_controls
Keywords: datasets
Description: ProbeIDs of low stringency controls
URL: ../../../library/beadarray/html/ls_controls.html

Entry: matrix.mean
Aliases: matrix.mean
Keywords: methods
Description: Calculate the mean of a matrix
URL: ../../../library/beadarray/html/matrix.mean.html

Entry: medianNormalise
Aliases: medianNormalise
Keywords: methods
Description: Median Normalisation for BeadLevelList objects
URL: ../../../library/beadarray/html/medianNormalise.html

Entry: neg_controls
Aliases: neg_controls
Keywords: datasets
Description: ProbeIDs of negative stringency controls
URL: ../../../library/beadarray/html/neg_controls.html

Entry: other_controls
Aliases: other_controls
Keywords: datasets
Description: ProbeIDs of other controls
URL: ../../../library/beadarray/html/other_controls.html

Entry: pairwiseMA
Aliases: pairwiseMA panel.XY panel.MA
Keywords: hplot
Description: Scatter plots and MA-plots for all specified arrays
URL: ../../../library/beadarray/html/pairwiseMA.html

Entry: plotArray
Aliases: plotArray
Keywords: hplot
Description: Plot outline of hexagonal array
URL: ../../../library/beadarray/html/plotArray.html

Entry: plotBeadIntensities
Aliases: plotBeadIntensities
Keywords: hplot
Description: Plot bead intensities
URL: ../../../library/beadarray/html/plotBeadIntensities.html

Entry: plotBeadLocations
Aliases: plotBeadLocations plotCoords
Keywords: hplot
Description: Show bead locations
URL: ../../../library/beadarray/html/plotBeadLocations.html

Entry: plotCluster
Aliases: plotCluster probeCluster
Keywords: hplot
Description: Clustering of bead position
URL: ../../../library/beadarray/html/plotCluster.html

Entry: plotDistances
Aliases: plotDistances
Keywords: methods
Description: Plot the distances between a set of co-ordinates
URL: ../../../library/beadarray/html/plotDistances.html

Entry: plotMA.beads
Aliases: plotMA.beads
Keywords: hplot
Description: Show MA plots
URL: ../../../library/beadarray/html/plotMA.beads.html

Entry: plotMAXY
Aliases: plotMAXY
Keywords: hplot
Description: Scatter plots and MA-plots for all specified arrays
URL: ../../../library/beadarray/html/plotMAXY.html

Entry: plotOnSAM
Aliases: plotOnSAM
Keywords: hplot
Description: Show variation between all 96 arrays on a SAM
URL: ../../../library/beadarray/html/plotOnSAM.html

Entry: plotProbeDistances
Aliases: plotProbeDistances
Keywords: methods
Description: Plot the distances between a set of beads
URL: ../../../library/beadarray/html/plotProbeDistances.html

Entry: plotProbeVariation
Aliases: plotProbeVariation
Keywords: methods
Description: Plot variation
URL: ../../../library/beadarray/html/plotProbeVariation.html

Entry: plotXY.beads
Aliases: plotXY.beads
Keywords: hplot
Description: XY plots for two samples
URL: ../../../library/beadarray/html/plotXY.beads.html

Entry: probeDiagnostics
Aliases: probeDiagnostics
Keywords: hplot
Description: Diagnostics plot for a bead type
URL: ../../../library/beadarray/html/probeDiagnostics.html

Entry: qsplineNormalise
Aliases: qsplineNormalise
Keywords: methods
Description: Qsplinw Normalisation for BeadLevelList objects
URL: ../../../library/beadarray/html/qsplineNormalise.html

Entry: quantileNormalise
Aliases: quantileNormalise normalizeBetweenArrays
Keywords: methods
Description: Quantile Normalisation for BeadLevelList objects
URL: ../../../library/beadarray/html/quantileNormalise.html

Entry: readBeadImages
Aliases: readBeadImages calculateBackground calculateForegroundIntensities sharpen averagePixels read.pgmfile
Keywords: IO
Description: Read BeadArray information into R
URL: ../../../library/beadarray/html/readBeadImages.html

Entry: readBeadSummaryData
Aliases: readBeadSummaryData readCols
Keywords: IO
Description: Read bead summary data information into R
URL: ../../../library/beadarray/html/readBeadSummaryData.html

Entry: readBeadSummaryTargets
Aliases: readBeadSummaryTargets
Keywords: IO
Description: Create targets object
URL: ../../../library/beadarray/html/readBeadSummaryTargets.html

Entry: readBeadTargets
Aliases: readBeadTargets
Keywords: IO
Description: Create targets object
URL: ../../../library/beadarray/html/readBeadTargets.html

Entry: readNonXYData
Aliases: readNonXYData
Keywords: IO
Description: Read BeadArray information into R
URL: ../../../library/beadarray/html/readNonXYData.html

Entry: readProbeInfo
Aliases: readProbeInfo
Keywords: hplot
Description: Read Probe Information
URL: ../../../library/beadarray/html/readProbeInfo.html

Entry: removeArrays
Aliases: removeArrays
Keywords: methods
Description: Finds unregistered beads
URL: ../../../library/beadarray/html/removeArrays.html

Entry: subsetting
Aliases: [.BeadLevelList [.BeadSummaryList printHead
Keywords: manip
Description: Subset BeadLevelList, BeadSummaryList
URL: ../../../library/beadarray/html/subsetting.html
