# Assessing array quality on spotted arrays

## Documentation for package `arrayQuality' version 1.10.0

## 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
BEbin.linear | 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
HsReferenceDB | Reference slides for Mouse oligos hybridizations
index.html | Reference slides for Mouse oligos hybridizations
maQualityPlots | Qualitative diagnostic plot for general hybridization
MEEBOctrl | Annotations and controls for the MEEBO set.
meeboQuality | Diagnostics plots designed for MEEBO set controls
meeboQualityPlots | Qualitative diagnostic plot for general hybridization, specific to MEEBO set.
MEEBOset | Annotations and controls for the MEEBO set.
MeeboSpotType.txt | Example GPR files
MeeboSpotTypes | Internal arrayQuality functions
MEEBOtiling | Annotations and controls for the MEEBO set.
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
qpBEplot.linear | Internal arrayQuality functions
qpBoxplotMeebo | Internal arrayQuality functions
qpDotPlots | 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
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
RDI108\_n.gpr | Example GPR files
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
StanfordDCV1.7complete.txt | Example GPR files
tilingres | Annotations and controls for the MEEBO set.