Quality control and low-level analysis of BeadArrays


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Documentation for package `beadarray' version 1.2.2

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averagePixels Read BeadArray information into R
backgroundCorrect Background Correct a BeadLevelList object
backgroundCorrect,BeadLevelList-method Background Correct a BeadLevelList object
backgroundCorrect,BeadLevelList-methods Background Correct a BeadLevelList object
backgroundNormalise Background Normalisation for Bead Summary Data objects
backgroundNormalise, ExpressionSetIllumina, ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
backgroundNormalise, ExpressionSetIllumina-method Background Normalisation for Bead Summary Data objects
backgroundNormalise, ExpressionSetIllumina-methods Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
BeadChipSummary Interactive bead level plotting
BeadLevelList-class Class "BeadLevelList"
BeadLevelNormalise Bead Level Normalisation
BLData BeadLevelList for the example experiment
BSData ExpressionSetIllumina object for the example experiment
calculateBackground Read BeadArray information into R
calculateForegroundIntensities Read BeadArray information into R
cbind.BeadLevelList Combine BeadLevelList or BeadSummaryList Objects
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.
createBeadSummaryData Produce bead averages
createBeadSummaryData, BeadLevelList-method Find Outliers
createBeadSummaryData,BeadLevelList-method Produce bead averages
createBeadSummaryDataSlow 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.
DiffScore Illumina's DE statistic
dim.BeadLevelList Retrieve the Dimensions of a BeadLevelList
dimnames.BeadLevelList Retrieve the Dimension Names of an BeadLevelList or BeadSummaryList Object
displayTIFFImage Display part of a TIFF Image
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 array
findAllOutliers, BeadLevelList-method Find Outliers
findAllOutliersSlow Find outliers on array
findBeadStatus Find Outliers
FindIlluminaSpotl Display part of a TIFF Image
getProbeIndices Find Outliers
getProbeIndicesC Find Outliers
getProbeIntensities Find Outliers
getProbeIntensities,BeadLevelList-method Find Outliers
IdentifyBeads Display part of a TIFF Image
IdentifyIntensity Display part of a TIFF Image
imageplot imageplot for BeadArrays object
imageplot, BeadLevelList-methods Class "BeadLevelList"
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.
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
plotQC Read and plot Illumina quality control information
plotXY XY plots for two samples
print.BeadLevelList Class "BeadLevelList"
QC Illumina quality control 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
rbind.BeadLevelList Combine BeadLevelList or BeadSummaryList Objects
read.pgmfile Read BeadArray information into R
readBeadLevelData Read BeadArray information into R
readBeadSummaryData Read bead summary data information into R
readBeadSummaryTargets Create targets object
readBeadTargets Create targets object
readCols Read bead summary data information into R
readQC Read and plot 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.
sharpen Read BeadArray information into R
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
showTIFF Display part of a TIFF Image
singleQCPlot Read and plot Illumina quality control information
[,ExpressionSetIllumina-method Class to Contain Objects Describing High-Throughput Illumina Expression BeadArrays.
[.BeadLevelList Class "BeadLevelList"