BLData                  BeadLevelList for the example experiment
BSData                  BeadSummaryList for the example experiment
BeadLevelList-class     Red, Green Intensity List - class
BeadSummaryList-class   Stores bead summary data - class
LargeDataObject-class   Large Data Object - class
[.BeadLevelList         Subset BeadLevelList, BeadSummaryList
backgroundCorrectBeads
                        Background Correct a BeadLevelList object
biotin_controls         ProbeIDs of Biotin controls
cbind.BeadLevelList     Combine BeadLevelList or BeadSummaryList
                        Objects
checkRandomness         Test for random distribution of co-ordinates
createBeadSummaryData   Produce bead averages
cy3_controls            ProbeIDs of cy3 controls
dim.BeadLevelList       Retrieve the Dimensions of an BeadLevelList or
                        BeadSummaryList
dimnames.BeadLevelList
                        Retrieve the Dimension Names of an
                        BeadLevelList or BeadSummaryList Object
displayTIFFImage        Display part of a TIFF Image
findAllOutliers         Find outliers on array
findBeadStatus          Find Outliers
findHighestChis         Find least randomly distributed beads
findHighestSD           Highest standard deviation.
findLowestCounts        Find Lowest bead counts
findMostOutliers        Beads with most outliers
getDimensions           Get dimension of an array
getMeanIntensities      Find Bead Type Averages
getProbeCoords          Find Bead Co-ordinates
getProbeIDs             Get unique ProbeIDs
getProbeInfo            Get information for ProbeID
getProbeIntensities     Get Intensites of Beads
getUnregisteredBeads    Finds unregistered beads
histBeadCounts          Plot numbers of each bead
housekeeping_controls   ProbeIDs of housekeeping controls
hs_controls             ProbeIDs of high stringency controls
labelling_controls      ProbeIDs of housekeeping controls
ls_controls             ProbeIDs of low stringency controls
matrix.mean             Calculate the mean of a matrix
medianNormalise         Median Normalisation for BeadLevelList objects
neg_controls            ProbeIDs of negative stringency controls
other_controls          ProbeIDs of other controls
pairwiseMA              Scatter plots and MA-plots for all specified
                        arrays
plotArray               Plot outline of hexagonal array
plotBeadIntensities     Plot bead intensities
plotBeadLocations       Show bead locations
plotCluster             Clustering of bead position
plotDistances           Plot the distances between a set of
                        co-ordinates
plotMA.beads            Show MA plots
plotMAXY                Scatter plots and MA-plots for all specified
                        arrays
plotOnSAM               Show variation between all 96 arrays on a SAM
plotProbeDistances      Plot the distances between a set of beads
plotProbeVariation      Plot variation
plotXY.beads            XY plots for two samples
probeDiagnostics        Diagnostics plot for a bead type
qsplineNormalise        Qsplinw Normalisation for BeadLevelList objects
quantileNormalise       Quantile Normalisation for BeadLevelList
                        objects
readBeadImages          Read BeadArray information into R
readBeadSummaryData     Read bead summary data information into R
readBeadSummaryTargets
                        Create targets object
readBeadTargets         Create targets object
readNonXYData           Read BeadArray information into R
readProbeInfo           Read Probe Information
removeArrays            Finds unregistered beads
