# Assessing array quality on spotted arrays

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

12Mm250.gpr | Example GPR files
9Mm137.gpr | Example GPR files
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 | Quality score and diagnostic plots for general hybridization
HsReferenceDB | Reference slides for Mouse oligos hybridizations
HsScalingTable | 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
MmScalingTable | 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
qualRefTable | General hybridization quality score scaling table
readGPR | Reading GenePix gpr file
replicatesAvariance | Internal arrayQuality functions
setCtlCol | Internal arrayQuality functions
slideQuality | Quality Control statistics for general hybridization