Assessing array quality on spotted arrays


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Documentation for package `arrayQuality' version 1.0.7

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12Mm250.gpr Example GPR files
9Mm137.gpr Example GPR files
agcontrolCode Diagnostic plots and comparative boxplots for general hybridization, Agilent format
agQuality Diagnostic plots and comparative boxplots for general hybridization, Agilent format
arrayControls Internal arrayQuality functions
arrayReplicates Internal arrayQuality functions
arrayScal Internal arrayQuality functions
EMSplit Internal arrayQuality functions
globalQuality Quality measures for general hybridization.
gpFlagWt Internal arrayQuality functions
gpQuality Diagnostic plots and comparative boxplots for general hybridization
HsReferenceDB Reference slides for Mouse oligos hybridizations
index.html Reference slides for Mouse oligos hybridizations
maQualityPlots Qualitative diagnostic plot for general hybridization
MmDEGenes Known DE genes for Mouse quality hybridizations.
MmReferenceDB Reference slides for Mouse oligos hybridizations
outputNormData Internal arrayQuality functions
PRv9mers Print Run Quality version 9mers
PRvQCHyb Print run Quality version Quality Control Hybridization
qpDotPlots Internal arrayQuality functions
qpHexbin Internal arrayQuality functions
qpImage Internal arrayQuality functions
qpMAPlots Internal arrayQuality functions
qpPTLoess Internal arrayQuality functions
qpS2N Internal arrayQuality functions
qualBoxplot Comparative boxplot for general hybridization Quality Control
quality2HTML Internal arrayQuality functions
qualityScore Quality Control score for general hybridization
readAgilent Extraction of measures from Agilent (.txt) files.
readcontrolCode Control status information
readGPR Reading GenePix gpr file
readSpot Extraction of measures from Spot (.spot) files.
replicatesAvariance Internal arrayQuality functions
scaleRefTable General hybridization quality scaling
setCtlCol Internal arrayQuality functions
slideQuality Quality Control statistics for general hybridization
spotQuality Diagnostic plots and comparative boxplots for general hybridization, Spot format