BASH                    BASH - BeadArray Subversion of Harshlight
BASHCompact             BASH - Compact Defect Analysis
BASHDiffuse             BASH - Diffuse Defect Analysis
BASHExtended            BASH - Extended Defect Analysis
BLData                  beadLevelData object from an example experiment
BSData                  ExpressionSetIllumina object for the example
                        experiment
BeadLevelList-class     Class "BeadLevelList"
ExpressionControlData   Control annotation for Illumina expression
                        chips
ExpressionSetIllumina-class
                        Class "ExpressionSetIllumina"
HULK                    HULK - Bead Array Normalization by
                        NEighbourhood Residuals
backgroundCorrectSingleSection
                        Background correct an array-section
beadLevelData-class     Class "beadLevelData"
beadStatusVector        Classify each bead according to its control
                        status
beadarrayUsersGuide     View beadarray User's Guide
calculateDetection      Calculate detection scores
calculateOutlierStats   Outlier distribution stats
checkRegistration       Perform check for misregistered array segments.
controlProbeDetection   Percentage of beads detected
controlProfile          Control annotation for Illumina expression
                        chips
convertBeadLevelList    Convert a BeadLevelList object into a
                        beadLevelData object
createBeadSummaryData   Deprecated Functions
createTargetsFile       A function to generate a targets file given a
                        directory of Illumina bead-level files
expressionQCPipeline    Flexible bead-level QC pipeline
generateNeighbours      Generate matrix of neighbouring beads
getAnnotation           Storage of annotation information
getBeadData             Get raw data from a beadLevelData object
illuminaChannel-class   Class "illuminaChannel"
illuminaOutlierMethod   Identifier outliers on an array section
imageplot               imageplot for beadLevelData object
insertBeadData          Add or modify data in a beadLevelData object
insertSectionData       Modify the sectionData slot
logRedChannelTransform
                        Functions for transforming the data store in a
                        'beadLevelData' object for easier visualisation
                        or summarisation.
makeQCTable             Tabulate QC scores
medianNormalise         Median normalise data in a matrix
normaliseIllumina       Normalise Illumina expression data
numBeads                Gets the number of beads from a beadLevelData
                        object
outlierplot             Plot outlier locations
plotBeadIntensities     Plotting the intensities of selected beads on a
                        section
plotBeadLocations       Plot bead locations
plotChipLayout          Function to Plot the Layout of an Illumina
                        BeadChip
plotMAXY                Scatter plots and MA-plots for all specified
                        arrays
plotTIFF                Produce plots of the Illumina tiff images
poscontPlot             Plot the positive controls
quickSummary            Create summary values for specified IDs
readBeadSummaryData     Read BeadStudio gene expression output
readIllumina            Read bead-level Illumina data
readLocsFile            Read ".locs" file.
readTIFF                Read the Illumina tiff images
sectionNames            Gets the section names from a beadLevelData
                        Object
setWeights              Set weights from BASH
showArrayMask           Show Array Mask
summarize               Create a summarized object
