Quality assessment and low-level analysis for Illumina BeadArray data


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Documentation for package ‘beadarray’ version 1.8.0

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arrayNames Gets the strip/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
beadarrayUsersGuide View beadarray User's Guide
BeadChipSummary Interactive bead-level plotting
BeadLevelList Class "BeadLevelList"
BeadLevelList-class Class "BeadLevelList"
beadResids Calculates per strip/array bead-level residuals
BLData BeadLevelList objec from an 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 from two BeadLevelList objects
combineBeadLevelLists,BeadLevelList-method Class "BeadLevelList"
copyBeadLevelList Copies a BeadLevelList Object
copyBeadLevelList,BeadLevelList-method Class "BeadLevelList"
createBeadSummaryData 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.
Detection<-,ExpressionSetIllumina,matrix-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,matrix-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
findAllOutliers Find outliers on a given strip/array
findBeadStatus Find Outliers
getArrayData Get raw data from a BeadLevelList object
getArrayData,BeadLevelList-method Class "BeadLevelList"
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 BeadLevelList object
initialize,BeadLevelList-method Class "BeadLevelList"
initialize,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
medianNormalise Median normalise data in a matrix
NoBeads Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
NoBeads<-,ExpressionSetIllumina,matrix-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 densities of bead intensities
plotBeadIntensities Plot bead intensities
plotBeadLocations Plot 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
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.
QCInfo<-,ExpressionSetIllumina,list-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
rankInvariantNormalise Rank Invariant normalise data in a matrix
readBeadSummaryData Read BeadStudio gene expression output
readBGX Read Illumina .bgx file into R
readIllumina Read bead-level data into R
readQC Read Illumina control intensities
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.
[,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
[[,BeadLevelList,ANY,missing-method Class "BeadLevelList"