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.