Quality control and low-level analysis of BeadArrays


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Documentation for package ‘beadarray’ version 1.6.0

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arrayNames Gets the array names from a BeadLevelList Object
arrayNames,BeadLevelList-method Class "BeadLevelList"
backgroundCorrect Background Correct a BeadLevelList object
backgroundCorrect,BeadLevelList,character,double,logical-method Class "BeadLevelList"
backgroundCorrect,BeadLevelList-method Background Correct a BeadLevelList object
backgroundCorrect,BeadLevelList-methods Background Correct a BeadLevelList object
backgroundNormalise, ExpressionSetIllumina,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
backgroundNormalise, ExpressionSetIllumina-methods Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
BeadChipSummary Interactive bead level plotting
BeadLevelList Class "BeadLevelList"
BeadLevelList-class Class "BeadLevelList"
beadResids Calculates per array bead-level residuals
BLData BeadLevelList for the example experiment
boxplotBeads Box plot of bead intensities
BSData ExpressionSetIllumina object for the example experiment
class:ExpressionSetIllumina Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
combine,ExpressionSetIllumina,ANY-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
combine,ExpressionSetIllumina,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
combineBeadLevelLists Combines data a BeadLevelList Object
combineBeadLevelLists,BeadLevelList-method Class "BeadLevelList"
copyBeadLevelList Copies a BeadLevelList Object
copyBeadLevelList,BeadLevelList-method Class "BeadLevelList"
createBeadSummaryData Produce bead averages
createBeadSummaryData, BeadLevelList-method Find Outliers
createBeadSummaryData,BeadLevelList-method Produce bead averages
Detection Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
Detection,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
dim,BeadLevelList-method Class "BeadLevelList"
ExpressionSetIllumina-class Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
exprs,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
exprs<-,ExpressionSetIllumina,ANY-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
exprs<-,ExpressionSetIllumina,matrix-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
findAllOutliers Find outliers on array
findAllOutliers, BeadLevelList-method Find Outliers
findAllOutliers-methods Find outliers on array
findBeadStatus Find Outliers
getArrayData Gets the raw data from a BeadLevelList object
getArrayData,BeadLevelList-method Class "BeadLevelList"
getProbeIndices Find Outliers
getProbeIndicesC Find Outliers
getProbeIntensities Find Outliers
getProbeIntensities,BeadLevelList-method Find Outliers
getVariance Gets the bead-type variances from an ExpressionSetIllumina Object
getVariance,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
imageplot imageplot for BeadArrays object
initialize,BeadLevelList-method Class "BeadLevelList"
initialize,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
LargeDataObject-class Large Data Object - class
medianNormalise Median Normalisation for BeadLevelList objects
NoBeads Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
normaliseIllumina Normalise Illumina expression data
numBeads Gets the number of beads from a BeadLevelList object
numBeads,BeadLevelList-method Class "BeadLevelList"
pData,BeadLevelList-method Class "BeadLevelList"
phenoData,BeadLevelList-method Class "BeadLevelList"
plotBeadDensities plot density of bead intensities
plotBeadIntensities Plot bead intensities
plotBeadLocations Show bead locations
plotMA Show MA plots
plotMAXY Scatter plots and MA-plots for all specified arrays
plotOnSAM Show variation between all 96 arrays
plotRG Plot bead level data: R vs G intensities
plotXY XY plots for two samples
QC Illumina quality control data
qcBeadLevel Generate simple diagnostic plots for Illumina bead level data
QCInfo Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
QCInfo,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
rankInvariantNormalise Rank Invariant Normalisation for Bead Summary data
readBeadSummaryData Read BeadStudio gene expression output
readBGX Read Illumina bgx file into R
readIllumina Read BeadArray information into R
readQC Read Illumina quality control information
SAMSummary Interactive bead level plotting
se.exprs,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
se.exprs<-,ExpressionSetIllumina,matrix-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
show,BeadLevelList-method Class "BeadLevelList"
show,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
show,LargeDataObject-method Large Data Object - class
[,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
[[,BeadLevelList,ANY,missing-method Class "BeadLevelList"