Entry: BASH
Aliases: BASH
Keywords: misc
Description: BASH - BeadArray Subversion of Harshlight
URL: ../../../library/beadarray/html/BASH.html

Entry: BASHCompact
Aliases: BASHCompact
Keywords: misc
Description: BASH - Compact Defect Analysis
URL: ../../../library/beadarray/html/BASHCompact.html

Entry: BASHDiffuse
Aliases: BASHDiffuse
Keywords: misc
Description: BASH - Diffuse Defect Analysis
URL: ../../../library/beadarray/html/BASHDiffuse.html

Entry: BASHExtended
Aliases: BASHExtended
Keywords: misc
Description: BASH - Extended Defect Analysis
URL: ../../../library/beadarray/html/BASHExtended.html

Entry: BGFilter
Aliases: BGFilter
Keywords: misc
Description: Background Filter
URL: ../../../library/beadarray/html/BGFilter.html

Entry: BGFilterWeighted
Aliases: BGFilterWeighted
Keywords: misc
Description: Weighted Background Filter
URL: ../../../library/beadarray/html/BGFilterWeighted.html

Entry: BLData
Aliases: BLData
Keywords: datasets
Description: BeadLevelList objec from an example experiment
URL: ../../../library/beadarray/html/BLData.html

Entry: BSData
Aliases: BSData
Keywords: datasets
Description: ExpressionSetIllumina object for the example experiment
URL: ../../../library/beadarray/html/BSData.html

Entry: ExpressionControlData
Aliases: ExpressionControlData
Keywords: datasets
Description: Control annotation for Illumina expression chips
URL: ../../../library/beadarray/html/ExpressionControlData.html

Entry: ArrayMask
Aliases: addArrayMask removeArrayMask clearArrayMask showArrayMask
Keywords: misc
Description: Array Mask
URL: ../../../library/beadarray/html/addArrayMask.html

Entry: arrayNames
Aliases: arrayNames
Keywords: manip
Description: Gets the strip/array names from a BeadLevelList Object
URL: ../../../library/beadarray/html/arrayNames.html

Entry: backgroundControlPlot
Aliases: backgroundControlPlot
Keywords: 
Description: QA measures based on bead-level negative controls
URL: ../../../library/beadarray/html/backgroundControlPlot.html

Entry: backgroundCorrect
Aliases: backgroundCorrect backgroundCorrect,BeadLevelList-method
Keywords: methods
Description: Background correct a BeadLevelList object
URL: ../../../library/beadarray/html/backgroundCorrect.html

Entry: beadResids
Aliases: beadResids
Keywords: manip
Description: Calculates per strip/array bead-level residuals
URL: ../../../library/beadarray/html/beadResids.html

Entry: beadarrayUsersGuide
Aliases: beadarrayUsersGuide
Keywords: documentation
Description: View beadarray User's Guide
URL: ../../../library/beadarray/html/beadarrayUsersGuide.html

Entry: boxplotBeads
Aliases: boxplotBeads
Keywords: hplot
Description: Box plot of bead intensities
URL: ../../../library/beadarray/html/boxplotBeads.html

Entry: calculateBeadLevelScores
Aliases: calculateBeadLevelScores gradientPlot
Keywords: 
Description: Quality assessment for expression chips
URL: ../../../library/beadarray/html/calculateBeadLevelScores.html

Entry: calculateDetection
Aliases: calculateDetection
Keywords: 
Description: Calculate detection scores
URL: ../../../library/beadarray/html/calculateDetection.html

Entry: chooseClusters
Aliases: chooseClusters
Keywords: misc
Description: Choose Clusters
URL: ../../../library/beadarray/html/chooseClusters.html

Entry: BeadLevelList-class
Aliases: BeadLevelList-class BeadLevelList show,BeadLevelList-method dim,BeadLevelList-method initialize,BeadLevelList-method arrayNames,BeadLevelList-method numBeads,BeadLevelList-method copyBeadLevelList,BeadLevelList-method combineBeadLevelLists,BeadLevelList-method pData,BeadLevelList-method phenoData,BeadLevelList-method [[,BeadLevelList,ANY,missing-method getArrayData,BeadLevelList-method backgroundCorrect,BeadLevelList,character,double,logical-method
Keywords: classes
Description: Class "BeadLevelList"
URL: ../../../library/beadarray/html/class-BeadLevelList.html

Entry: ExpressionSetIllumina
Aliases: class:ExpressionSetIllumina ExpressionSetIllumina-class exprs,ExpressionSetIllumina-method exprs<-,ExpressionSetIllumina,matrix-method se.exprs,ExpressionSetIllumina-method se.exprs<-,ExpressionSetIllumina,matrix-method NoBeads NoBeads,ExpressionSetIllumina-method NoBeads<- NoBeads<-,ExpressionSetIllumina,matrix-method Detection Detection,ExpressionSetIllumina-method Detection<- Detection<-,ExpressionSetIllumina,matrix-method QCInfo QCInfo<- QCInfo<-,ExpressionSetIllumina,list-method QCInfo,ExpressionSetIllumina-method [,ExpressionSetIllumina-method initialize,ExpressionSetIllumina-method combine,ExpressionSetIllumina,ExpressionSetIllumina-method combine,ExpressionSetIllumina,ANY-method show,ExpressionSetIllumina-method getVariance,ExpressionSetIllumina-method
Keywords: classes
Description: Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
URL: ../../../library/beadarray/html/class.ExpressionSetIllumina.html

Entry: closeImage
Aliases: closeImage
Keywords: misc
Description: Close Image
URL: ../../../library/beadarray/html/closeImage.html

Entry: combineBeadLevelLists
Aliases: combineBeadLevelLists
Keywords: manip
Description: Combines data from two BeadLevelList objects
URL: ../../../library/beadarray/html/combineBeadLevelLists.html

Entry: copyBeadLevelList
Aliases: copyBeadLevelList
Keywords: manip
Description: Copies a BeadLevelList Object
URL: ../../../library/beadarray/html/copyBeadLevelLists.html

Entry: createBeadSummaryData
Aliases: createBeadSummaryData
Keywords: methods
Description: Produce bead averages
URL: ../../../library/beadarray/html/createBeadSummaryData.html

Entry: denseRegions
Aliases: denseRegions
Keywords: misc
Description: Find Dense Regions of Points (as used in diffuse defect analysis).
URL: ../../../library/beadarray/html/denseRegions.html

Entry: findAllOutliers
Aliases: findAllOutliers
Keywords: methods
Description: Find outliers on a given strip/array
URL: ../../../library/beadarray/html/findAllOutliers.html

Entry: findBeadStatus
Aliases: findBeadStatus getProbeIntensities getProbeIntensities,BeadLevelList-method
Keywords: methods
Description: Find Outliers
URL: ../../../library/beadarray/html/findBeadStatus.html

Entry: generateE
Aliases: generateE
Keywords: misc
Description: Generate Error Image for BeadLevelList object
URL: ../../../library/beadarray/html/generateE.html

Entry: generateNeighbours
Aliases: generateNeighbours
Keywords: misc
Description: Generate Neighbours Matrix for BeadLevelList object
URL: ../../../library/beadarray/html/generateNeighbours.html

Entry: getAnnotation
Aliases: getAnnotation getControlAnno setAnnotation
Keywords: 
Description: Storage of annotation information for Illumina expression chips
URL: ../../../library/beadarray/html/getAnnotation.html

Entry: getArrayData
Aliases: getArrayData
Keywords: manip
Description: Get raw data from a BeadLevelList object
URL: ../../../library/beadarray/html/getArrayData.html

Entry: getVariance
Aliases: getVariance
Keywords: manip
Description: Gets the bead-type variances from an ExpressionSetIllumina Object
URL: ../../../library/beadarray/html/getVariance.html

Entry: imageplot
Aliases: imageplot
Keywords: hplot
Description: imageplot for BeadLevelList object
URL: ../../../library/beadarray/html/imageplot.html

Entry: interactivePlots
Aliases: BeadChipSummary SAMSummary
Keywords: hplot
Description: Interactive bead-level plotting
URL: ../../../library/beadarray/html/interactivePlots.html

Entry: lmhPlot
Aliases: lmhPlot
Keywords: 
Description: Plot the bead-level hybridisation controls
URL: ../../../library/beadarray/html/lmhPlot.html

Entry: medianNormalise
Aliases: medianNormalise
Keywords: methods
Description: Median normalise data in a matrix
URL: ../../../library/beadarray/html/medianNormalise.html

Entry: normaliseIllumina
Aliases: normaliseIllumina
Keywords: methods
Description: Normalise Illumina expression data
URL: ../../../library/beadarray/html/normaliseIllumina.html

Entry: numBeads
Aliases: numBeads
Keywords: manip
Description: Gets the number of beads from a BeadLevelList object
URL: ../../../library/beadarray/html/numBeads.html

Entry: outlierPlot
Aliases: outlierPlot
Keywords: 
Description: Locations of outliers on an Illumina chip
URL: ../../../library/beadarray/html/outlierplot.html

Entry: plotBeadDensities
Aliases: plotBeadDensities
Keywords: hplot
Description: plot densities of bead intensities
URL: ../../../library/beadarray/html/plotBeadDensities.html

Entry: plotBeadIntensities
Aliases: plotBeadIntensities
Keywords: hplot
Description: Plot bead intensities
URL: ../../../library/beadarray/html/plotBeadIntensities.html

Entry: plotBeadLocations
Aliases: plotBeadLocations
Keywords: hplot
Description: Plot bead locations
URL: ../../../library/beadarray/html/plotBeadLocations.html

Entry: plotMA
Aliases: plotMA
Keywords: hplot
Description: Show MA plots
URL: ../../../library/beadarray/html/plotMA.html

Entry: plotMAXY
Aliases: plotMAXY
Keywords: hplot
Description: Scatter plots and MA-plots for all specified arrays
URL: ../../../library/beadarray/html/plotMAXY.html

Entry: plotOnSAM
Aliases: plotOnSAM
Keywords: hplot
Description: Show variation between all 96 arrays
URL: ../../../library/beadarray/html/plotOnSAM.html

Entry: plotRG
Aliases: plotRG
Keywords: hplot
Description: Plot bead-level data: R vs G intensities
URL: ../../../library/beadarray/html/plotRG.html

Entry: plotXY
Aliases: plotXY
Keywords: hplot
Description: XY plots for two samples
URL: ../../../library/beadarray/html/plotXY.html

Entry: poscontPlot
Aliases: poscontPlot
Keywords: 
Description: Plot bead-level housekeeping and biotin controls
URL: ../../../library/beadarray/html/poscontPlot.html

Entry: probePairsPlot
Aliases: probePairsPlot
Keywords: 
Description: QA plot using perfect match and mismatch controls
URL: ../../../library/beadarray/html/probePairsPlot.html

Entry: qcBeadLevel
Aliases: qcBeadLevel
Keywords: hplot
Description: Generate simple diagnostic plots for Illumina bead-level data
URL: ../../../library/beadarray/html/qcBeadLevel.html

Entry: rankIvariantNormalise
Aliases: rankInvariantNormalise
Keywords: methods
Description: Rank Invariant normalise data in a matrix
URL: ../../../library/beadarray/html/rankInvariantNormalise.html

Entry: readBGX
Aliases: readBGX
Keywords: IO
Description: Read Illumina .bgx file into R
URL: ../../../library/beadarray/html/readBGX.html

Entry: readBeadSummaryData
Aliases: readBeadSummaryData
Keywords: IO
Description: Read BeadStudio gene expression output
URL: ../../../library/beadarray/html/readBeadSummaryData.html

Entry: readIllumina
Aliases: readIllumina
Keywords: IO
Description: Read bead-level data into R
URL: ../../../library/beadarray/html/readIllumina.html

Entry: readQC
Aliases: readQC
Keywords: methods
Description: Read Illumina control intensities
URL: ../../../library/beadarray/html/readQC.html

Entry: setWeights
Aliases: setWeights
Keywords: misc
Description: Set BeadLevelList Weights
URL: ../../../library/beadarray/html/setWeights.html

Entry: viewBeads
Aliases: viewBeads
Keywords: hplot
Description: View Beads
URL: ../../../library/beadarray/html/viewBeads.html
