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

Entry: BeadLevelList-class
Aliases: BeadLevelList-class show, BeadLevelList-method initialize,BeadLevelList-method imageplot, BeadLevelList-methods [.BeadLevelList print.BeadLevelList
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,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: createBeadSummaryData
Aliases: createBeadSummaryData,BeadLevelList-method createBeadSummaryDataSlow createBeadSummaryData
Keywords: methods
Description: Produce bead averages
URL: ../../../library/beadarray/html/createBeadSummaryData.html

Entry: dim
Aliases: dim.BeadLevelList
Keywords: array
Description: Retrieve the Dimensions of a BeadLevelList
URL: ../../../library/beadarray/html/dim.html

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

Entry: findAllOutliers
Aliases: findAllOutliers findAllOutliersSlow
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: 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: 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: plotXY
Aliases: plotXY
Keywords: hplot
Description: XY plots for two samples
URL: ../../../library/beadarray/html/plotXY.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 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: readQC
Aliases: readQC plotQC plotQC.figure1 plotQC.figure2 plotQC.figure3 plotQC.figure4 plotQC.figure5 plotQC.figure6 singleQCPlot
Keywords: methods
Description: Read and plot Illumina quality control information
URL: ../../../library/beadarray/html/readQC.html
