BASH                    BASH - BeadArray Subversion of Harshlight
BASHCompact             BASH - Compact Defect Analysis
BASHDiffuse             BASH - Diffuse Defect Analysis
BASHExtended            BASH - Extended Defect Analysis
BeadLevelList-class     Class "BeadLevelList"
ExpressionSetIllumina-class
                        Class "ExpressionSetIllumina"
HULK                    HULK - Bead Array Normalization by
                        NEighbourhood Residuals
addFeatureData          Add probe data
annotation,beadLevelData-method
                        Storage of annotation information
backgroundCorrectSingleSection
                        Background correct an array-section
beadLevelData-class     Class "beadLevelData"
beadRegistrationData-class
                        Class "beadRegistrationData"
beadarray-package       The beadarray package: a tool for low-level
                        analysis of Illumina BeadArrays
beadarrayUsersGuide     View beadarray User's Guide
boxplot,ExpressionSetIllumina-method
                        Boxplots from summary data
calculateDetection      Calculate detection scores
calculateOutlierStats   Outlier distribution stats
checkRegistration       Perform check for misregistered array segments.
combine,beadLevelData,beadLevelData-method
                        Combine two objects.
controlProbeDetection   Percentage of beads detected
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
dim,beadLevelData-method
                        Retrieve the dimensions of an object
expressionQCPipeline    Flexible bead-level QC pipeline
generateNeighbours      Generate matrix of neighbouring beads
getBeadData             Get raw data from a beadLevelData object
identifyControlBeads    Classify each bead according to its control
                        status
illuminaChannel-class   Class "illuminaChannel"
illuminaForeground      Image processing functions
illuminaOutlierMethod   Identifier outliers on an array section
imageplot               imageplot for beadLevelData object
insertBeadData          Add, modify or remove data in a beadLevelData
                        object
insertSectionData       Modify the sectionData slot
limmaDE                 Differential expression using limma
limmaResults-class      Class "limmaResults"
logRedChannelTransform
                        Functions for transforming the data store in a
                        'beadLevelData' object for easier visualisation
                        or summarisation.
makeControlProfile      Retrieve control beads
makeGEOSubmissionFiles
                        Create files for a Gene Expression Omnibus
                        submission
makeQCTable             Tabulate QC scores
medianNormalise         Median normalise data in a matrix
metaTemplate            GEO required fields
metrics                 Accessing metrics information in bead-level
                        objects
noOutlierMethod         returns no outliers on an array section
normaliseIllumina       Normalise Illumina expression data
numBeads                Gets the number of beads from a beadLevelData
                        object
outlierplot             Plot outlier locations
platformSigs            Annotation definitions
plotBeadIntensities     Plotting the intensities of selected beads on a
                        section
plotBeadLocations       Plot bead locations
plotChipLayout          Function to Plot the Layout of an Illumina
                        BeadChip
plotMA,ExpressionSetIllumina-method
                        Function to construct the classic MA plots from
                        a dataset
plotMAXY                Scatter plots and MA-plots for all specified
                        arrays
plotTIFF                Produce plots of the Illumina tiff images
poscontPlot             Plot the positive controls
processSwathData        Prepare iScan data for use with beadarray
quickSummary            Create summary values for specified IDs
readBeadSummaryData     Read BeadStudio gene expression output
readIdatFiles           Read BeadScan gene expression output
readIllumina            Read bead-level Illumina data
readLocsFile            Read ".locs" file.
readSampleSheet         Read a Sample sheet for a BeadArray experiment
readTIFF                Read the Illumina tiff images
sectionNames            Gets the section names from a beadLevelData
                        Object
setWeights              Set weights from BASH
show,beadLevelData-method
                        Display object summary
showArrayMask           Show Array Mask
squeezedVarOutlierMethod
                        Identifier outliers on an array section
summarize               Create a summarized object
weightsOutlierMethod    returns all beads with weight=0.
