Assessing array quality on spotted arrays


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Documentation for package ‘arrayQuality’ version 1.84.0

Help Pages

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
BEbin.linear Internal arrayQuality functions
controlCodeHeebo Internal arrayQuality functions
controlCodeMeebo Internal arrayQuality functions
EMSplit Internal arrayQuality functions
getSpikeIds Internal arrayQuality functions
getSpikeIndex Internal arrayQuality functions
globalQuality Quality measures for general hybridization.
gpFlagWt Internal arrayQuality functions
gpQuality Diagnostic plots and comparative boxplots for general hybridization
heeboQuality Diagnostics plots designed for HEEBO set controls
heeboQualityPlots Qualitative diagnostic plot for general hybridization, specific to HEEBO set.
HeeboSpotTypes Internal arrayQuality functions
HsReferenceDB Reference slides for Mouse oligos hybridizations
index.html Reference slides for Mouse oligos hybridizations
maQualityPlots Qualitative diagnostic plot for general hybridization
meeboQuality Diagnostics plots designed for MEEBO set controls
meeboQualityPlots Qualitative diagnostic plot for general hybridization, specific to MEEBO set.
MeeboSpotTypes Internal arrayQuality functions
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
qcScore Quality Control score for general hybridization
qpBEplot.linear Internal arrayQuality functions
qpBoxplotMeebo Internal arrayQuality functions
qpDotPlots Internal arrayQuality functions
qpDotPlotsEEBO Internal arrayQuality functions
qpDotPlotsMeebo Internal arrayQuality functions
qpDotPlotsMeebo2 Internal arrayQuality functions
qpHexbin Internal arrayQuality functions
qpImage Internal arrayQuality functions
qpMAPlots Internal arrayQuality functions
qpMisMatchPlot Internal arrayQuality functions
qpPTLoess Internal arrayQuality functions
qpS2N Internal arrayQuality functions
qpS2Neebo Internal arrayQuality functions
qpS2Nmeebo Internal arrayQuality functions
qpTiling 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.
readAllSpikes Internal arrayQuality functions
readcontrolCode Control status information
readGPR Reading GenePix gpr file
readSpikeTypes Read Spike Types 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
Spike.Cy5vsCy3 Internal arrayQuality functions
Spike.Individual.Sensitivity Internal arrayQuality functions
Spike.MM.Scatter Internal arrayQuality functions
Spike.MMplot Internal arrayQuality functions
Spike.Sensitivity Internal arrayQuality functions
spotQuality Diagnostic plots and comparative boxplots for general hybridization, Spot format