# Assessing array quality on spotted arrays

## Documentation for package `arrayQuality' version 1.0.11

## User Guides and Package Vignettes

Read overview or browse directory.

## 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
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