BLData                  BeadLevelList objec from an example experiment
BSData                  ExpressionSetIllumina object for the example
                        experiment
BeadChipSummary         Interactive bead-level plotting
BeadLevelList-class     Class "BeadLevelList"
arrayNames              Gets the strip/array names from a BeadLevelList
                        Object
backgroundCorrect       Background correct a BeadLevelList object
beadResids              Calculates per strip/array bead-level residuals
beadarrayUsersGuide     View beadarray User's Guide
boxplotBeads            Box plot of bead intensities
class:ExpressionSetIllumina
                        Class to Contain Objects Describing
                        High-Throughput Illumina Expression BeadArrays.
combineBeadLevelLists   Combines data from two BeadLevelList objects
copyBeadLevelList       Copies a BeadLevelList Object
createBeadSummaryData   Produce bead averages
findAllOutliers         Find outliers on a given strip/array
findBeadStatus          Find Outliers
getArrayData            Get raw data from a BeadLevelList object
getVariance             Gets the bead-type variances from an
                        ExpressionSetIllumina Object
imageplot               imageplot for BeadLevelList object
medianNormalise         Median normalise data in a matrix
normaliseIllumina       Normalise Illumina expression data
numBeads                Gets the number of beads from a BeadLevelList
                        object
plotBeadDensities       plot densities of bead intensities
plotBeadIntensities     Plot bead intensities
plotBeadLocations       Plot 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 normalise data in a matrix
readBGX                 Read Illumina .bgx file into R
readBeadSummaryData     Read BeadStudio gene expression output
readIllumina            Read bead-level data into R
readQC                  Read Illumina control intensities
