BLData                  BeadLevelList for the example experiment
BSData                  ExpressionSetIllumina object for the example
                        experiment
BeadChipSummary         Interactive bead level plotting
BeadLevelList-class     Class "BeadLevelList"
BeadLevelNormalise      Bead Level Normalisation
DiffScore               Illumina's DE statistic
LargeDataObject-class   Large Data Object - class
QC                      Illumina quality control data
arrayNames              Gets the array names from a BeadLevelList
                        Object
backgroundCorrect       Background Correct a BeadLevelList object
backgroundNormalise     Background Normalisation for Bead Summary Data
                        objects
backgroundNormalise, ExpressionSetIllumina-methods
                        Class to Contain Objects Describing
                        High-Throughput Illumina Expression BeadArrays.
boxplotBeads            Box plot of bead intensities
combineBeadLevelLists   Combines data a BeadLevelList Object
copyBeadLevelList       Copies a BeadLevelList Object
createBeadSummaryData   Produce bead averages
displayTIFFImage        Display part of a TIFF Image
findAllOutliers         Find outliers on array
findBeadStatus          Find Outliers
getArrayData            Gets the raw intensity data from a
                        BeadLevelList object
imageplot               imageplot for BeadArrays object
medianNormalise         Median Normalisation for BeadLevelList objects
numBeads                Gets the number of beads from a BeadLevelList
                        object
plotBeadDensities       plot density of bead intensities
plotBeadIntensities     Plot bead intensities
plotBeadLocations       Show bead locations
plotMA                  Show MA plots
plotMAXY                Scatter plots and MA-plots for all specified
                        arrays
plotOnSAM               Show variation between all 96 arrays
plotRG                  Plot bead level data: R vs G intensities
plotXY                  XY plots for two samples
qcBeadLevel             Generate simple diagnostic plots for Illumina
                        bead level data
rankInvariantNormalise
                        Rank Invariant Normalisation for Bead Summary
                        data
readBeadLevelData       Read BeadArray information into R
readBeadSummaryData     Read BeadStudio gene expression output
readBeadSummaryTargets
                        Create targets object
readBeadTargets         Create targets object
readIllumina            Read BeadArray information into R
readQC                  Read Illumina quality control information
