BLData                  BeadLevelList for the example experiment
BSData                  ExpressionSetIllumina object for the example
                        experiment
BeadChipSummary         Interactive bead level plotting
BeadLevelList-class     Class "BeadLevelList"
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, ExpressionSetIllumina-methods
                        Class to Contain Objects Describing
                        High-Throughput Illumina Expression BeadArrays.
beadResids              Calculates per array bead-level residuals
boxplotBeads            Box plot of bead intensities
combineBeadLevelLists   Combines data a BeadLevelList Object
copyBeadLevelList       Copies a BeadLevelList Object
createBeadSummaryData   Produce bead averages
findAllOutliers         Find outliers on array
findBeadStatus          Find Outliers
getArrayData            Gets the raw data from a BeadLevelList object
getVariance             Gets the bead-type variances from an
                        ExpressionSetIllumina Object
imageplot               imageplot for BeadArrays object
medianNormalise         Median Normalisation for BeadLevelList objects
normaliseIllumina       Normalise Illumina expression data
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
readBGX                 Read Illumina bgx file into R
readBeadSummaryData     Read BeadStudio gene expression output
readIllumina            Read BeadArray information into R
readQC                  Read Illumina quality control information
