BASH                    BASH - BeadArray Subversion of Harshlight
BASHCompact             BASH - Compact Defect Analysis
BASHDiffuse             BASH - Diffuse Defect Analysis
BASHExtended            BASH - Extended Defect Analysis
BGFilter                Background Filter
BGFilterWeighted        Weighted Background Filter
BLData                  BeadLevelList objec from an example experiment
BSData                  ExpressionSetIllumina object for the example
                        experiment
BeadChipSummary         Interactive bead-level plotting
BeadLevelList-class     Class "BeadLevelList"
ExpressionControlData   Control annotation for Illumina expression
                        chips
HULK                    HULK - Bead Array Normalization by
                        NEighbourhood Residuals
HULKResids              HULK - Residuals
addArrayMask            Array Mask
arrayNames              Gets the strip/array names from a BeadLevelList
                        Object
backgroundControlPlot   QA measures based on bead-level negative
                        controls
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
calculateBeadLevelScores
                        Quality assessment for expression chips
calculateDetection      Calculate detection scores
chooseClusters          Choose Clusters
class:ExpressionSetIllumina
                        Class to Contain Objects Describing
                        High-Throughput Illumina Expression BeadArrays.
closeImage              Close Image
combineBeadLevelLists   Combines data from two BeadLevelList objects
copyBeadLevelList       Copies a BeadLevelList Object
createBeadSummaryData   Produce bead averages
denseRegions            Find Dense Regions of Points (as used in
                        diffuse defect analysis).
findAllOutliers         Find outliers on a given strip/array
findBeadStatus          Find Outliers
generateE               Generate Error Image for BeadLevelList object
generateNeighbours      Generate Neighbours Matrix for BeadLevelList
                        object
getAnnotation           Storage of annotation information for Illumina
                        expression chips
getArrayData            Get raw data from a BeadLevelList object
getVariance             Gets the bead-type variances from an
                        ExpressionSetIllumina Object
imageplot               imageplot for BeadLevelList object
lmhPlot                 Plot the bead-level hybridisation controls
medianNormalise         Median normalise data in a matrix
normaliseIllumina       Normalise Illumina expression data
numBeads                Gets the number of beads from a BeadLevelList
                        object
outlierPlot             Locations of outliers on an Illumina chip
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
poscontPlot             Plot bead-level housekeeping and biotin
                        controls
probePairsPlot          QA plot using perfect match and mismatch
                        controls
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
setWeights              Set BeadLevelList Weights
viewBeads               View Beads
