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: ExpressionSetIllumina object for the example experiment
URL: ../../../library/beadarray/html/BSData.html

Entry: BeadLevelNormalise
Aliases: BeadLevelNormalise
Keywords: methods
Description: Bead Level Normalisation
URL: ../../../library/beadarray/html/BeadLevelNormalise.html

Entry: DiffScore
Aliases: DiffScore
Keywords: IO
Description: Illumina's DE statistic
URL: ../../../library/beadarray/html/DiffScore.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: QC
Aliases: QC
Keywords: datasets
Description: Illumina quality control data
URL: ../../../library/beadarray/html/QC.html

Entry: arrayNames
Aliases: arrayNames
Keywords: manip
Description: Gets the array names from a BeadLevelList Object
URL: ../../../library/beadarray/html/arrayNames.html

Entry: backgroundCorrect
Aliases: backgroundCorrect backgroundCorrect,BeadLevelList-methods backgroundCorrect,BeadLevelList-method
Keywords: methods
Description: Background Correct a BeadLevelList object
URL: ../../../library/beadarray/html/backgroundCorrect.html

Entry: backgroundNormalise
Aliases: backgroundNormalise backgroundNormalise, ExpressionSetIllumina-method
Keywords: methods
Description: Background Normalisation for Bead Summary Data objects
URL: ../../../library/beadarray/html/backgroundNormalise.html

Entry: boxplotBeads
Aliases: boxplotBeads
Keywords: hplot
Description: Box plot of bead intensities
URL: ../../../library/beadarray/html/boxplotBeads.html

Entry: BeadLevelList-class
Aliases: BeadLevelList-class BeadLevelList show,BeadLevelList-method dim,BeadLevelList-method initialize,BeadLevelList-method arrayNames,BeadLevelList-method numBeads,BeadLevelList-method copyBeadLevelList,BeadLevelList-method combineBeadLevelLists,BeadLevelList-method pData,BeadLevelList-method phenoData,BeadLevelList-method [[,BeadLevelList,ANY,missing-method getArrayData,BeadLevelList-method backgroundCorrect,BeadLevelList,character,double,logical-method
Keywords: classes
Description: Class "BeadLevelList"
URL: ../../../library/beadarray/html/class-BeadLevelList.html

Entry: ExpressionSetIllumina
Aliases: backgroundNormalise, ExpressionSetIllumina-methods backgroundNormalise, ExpressionSetIllumina,ExpressionSetIllumina-method class:ExpressionSetIllumina ExpressionSetIllumina-class exprs<-,ExpressionSetIllumina,ANY-method exprs<-,ExpressionSetIllumina,matrix-method se.exprs<-,ExpressionSetIllumina,matrix-method exprs,ExpressionSetIllumina-method se.exprs,ExpressionSetIllumina-method QCInfo QCInfo,ExpressionSetIllumina-method [,ExpressionSetIllumina-method initialize,ExpressionSetIllumina-method combine,ExpressionSetIllumina,ExpressionSetIllumina-method combine,ExpressionSetIllumina,ANY-method show,ExpressionSetIllumina-method NoBeads,ExpressionSetIllumina-method Detection,ExpressionSetIllumina-method NoBeads Detection
Keywords: classes
Description: Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
URL: ../../../library/beadarray/html/class.ExpressionSetIllumina.html

Entry: combineBeadLevelLists
Aliases: combineBeadLevelLists
Keywords: manip
Description: Combines data a BeadLevelList Object
URL: ../../../library/beadarray/html/combineBeadLevelLists.html

Entry: copyBeadLevelList
Aliases: copyBeadLevelList
Keywords: manip
Description: Copies a BeadLevelList Object
URL: ../../../library/beadarray/html/copyBeadLevelLists.html

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

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

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

Entry: findBeadStatus
Aliases: findBeadStatus getProbeIndices getProbeIndicesC getProbeIntensities,BeadLevelList-method getProbeIntensities findAllOutliers, BeadLevelList-method createBeadSummaryData, BeadLevelList-method
Keywords: methods
Description: Find Outliers
URL: ../../../library/beadarray/html/findBeadStatus.html

Entry: getArrayData
Aliases: getArrayData
Keywords: manip
Description: Gets the raw intensity data from a BeadLevelList object
URL: ../../../library/beadarray/html/getArrayData.html

Entry: imageplot
Aliases: imageplot
Keywords: hplot
Description: imageplot for BeadArrays object
URL: ../../../library/beadarray/html/imageplot.html

Entry: interactivePlots
Aliases: BeadChipSummary SAMSummary
Keywords: hplot
Description: Interactive bead level plotting
URL: ../../../library/beadarray/html/interactivePlots.html

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

Entry: numBeads
Aliases: numBeads
Keywords: manip
Description: Gets the number of beads from a BeadLevelList object
URL: ../../../library/beadarray/html/numBeads.html

Entry: plotBeadDensities
Aliases: plotBeadDensities
Keywords: hplot
Description: plot density of bead intensities
URL: ../../../library/beadarray/html/plotBeadDensities.html

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

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

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

Entry: plotRG
Aliases: plotRG
Keywords: hplot
Description: Plot bead level data: R vs G intensities
URL: ../../../library/beadarray/html/plotRG.html

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

Entry: qcBeadLevel
Aliases: qcBeadLevel
Keywords: hplot
Description: Generate simple diagnostic plots for Illumina bead level data
URL: ../../../library/beadarray/html/qcBeadLevel.html

Entry: rankIvariantNormalise
Aliases: rankInvariantNormalise
Keywords: methods
Description: Rank Invariant Normalisation for Bead Summary data
URL: ../../../library/beadarray/html/rankInvariantNormalise.html

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

Entry: readBeadSummaryData
Aliases: readBeadSummaryData
Keywords: IO
Description: Read BeadStudio gene expression output
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: readIllumina
Aliases: readIllumina
Keywords: IO
Description: Read BeadArray information into R
URL: ../../../library/beadarray/html/readIllumina.html

Entry: readQC
Aliases: readQC
Keywords: methods
Description: Read Illumina quality control information
URL: ../../../library/beadarray/html/readQC.html
