arrayQuality: Assessing array quality on spotted arrays

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Functions for performing print-run and array level quality assessment.

Author
Agnes Paquet and Jean Yee Hwa Yang <yeehwa@stat.berkeley.edu>
Date of publication
None
Maintainer
Agnes Paquet <paquetagnes@yahoo.com>
License
LGPL
Version
1.52.0
URLs

View on Bioconductor

Man pages

agQuality
Diagnostic plots and comparative boxplots for general...
arrayQuality-internal
Internal arrayQuality functions
globalQuality
Quality measures for general hybridization.
gpQuality
Diagnostic plots and comparative boxplots for general...
gprDB
Reference slides for Mouse oligos hybridizations
heeboQuality
Diagnostics plots designed for HEEBO set controls
heeboQualityPlots
Qualitative diagnostic plot for general hybridization,...
maQualityPlots
Qualitative diagnostic plot for general hybridization
meeboQuality
Diagnostics plots designed for MEEBO set controls
meeboQualityPlots
Qualitative diagnostic plot for general hybridization,...
MmDEGenes
Known DE genes for Mouse quality hybridizations.
prdata
Example GPR files
PRv9mers
Print Run Quality version 9mers
PRvQCHyb
Print run Quality version Quality Control Hybridization
qcScore
Quality Control score for general hybridization
qualBoxplot
Comparative boxplot for general hybridization Quality Control
qualityScore
Quality Control score for general hybridization
readAgilent
Extraction of measures from Agilent (.txt) files.
readcontrolCode
Control status information
readGPR
Reading GenePix gpr file
readSpikeTypes
Read Spike Types File
readSpot
Extraction of measures from Spot (.spot) files.
scaleRefTable
General hybridization quality scaling
slideQuality
Quality Control statistics for general hybridization
spotQuality
Diagnostic plots and comparative boxplots for general...

Files in this package

arrayQuality/DESCRIPTION
arrayQuality/NAMESPACE
arrayQuality/R
arrayQuality/R/PRQCv1.R
arrayQuality/R/PRQCv2.R
arrayQuality/R/agQuality.R
arrayQuality/R/arrayControl.R
arrayQuality/R/gpQuality.R
arrayQuality/R/heeboQuality.R
arrayQuality/R/heeboSetQC.R
arrayQuality/R/meeboQuality.R
arrayQuality/R/qpHeeboFunc.R
arrayQuality/R/qpHexbin.R
arrayQuality/R/qpMeeboFunc.R
arrayQuality/R/qualFunc.R
arrayQuality/R/qualityPlots.R
arrayQuality/R/spikeIn.R
arrayQuality/R/spotQuality.R
arrayQuality/data
arrayQuality/data/HsReferenceDB.RData
arrayQuality/data/MmDEGenes.RData
arrayQuality/data/MmReferenceDB.RData
arrayQuality/inst
arrayQuality/inst/Heebo
arrayQuality/inst/Heebo/63421.gpr
arrayQuality/inst/Heebo/DCV2.0June06.txt
arrayQuality/inst/Heebo/hoc.gal
arrayQuality/inst/Meebo
arrayQuality/inst/Meebo/MeeboSpotType.txt
arrayQuality/inst/Meebo/RDI108_n.gpr
arrayQuality/inst/Meebo/StanfordDCV1.7complete.txt
arrayQuality/inst/gprQCData
arrayQuality/inst/gprQCData/12Mm250.gpr
arrayQuality/inst/gprQCData/9Mm137.gpr
arrayQuality/inst/gprQCData/index.html
arrayQuality/man
arrayQuality/man/MmDEGenes.Rd
arrayQuality/man/PRv9mers.Rd
arrayQuality/man/PRvQCHyb.Rd
arrayQuality/man/agQuality.Rd
arrayQuality/man/arrayQuality-internal.Rd
arrayQuality/man/globalQuality.Rd
arrayQuality/man/gpQuality.Rd
arrayQuality/man/gprDB.Rd
arrayQuality/man/heeboQuality.Rd
arrayQuality/man/heeboQualityPlots.Rd
arrayQuality/man/maQualityPlots.Rd
arrayQuality/man/meeboQuality.Rd
arrayQuality/man/meeboQualityPlots.Rd
arrayQuality/man/prdata.Rd
arrayQuality/man/qcScore.Rd
arrayQuality/man/qualBoxplot.Rd
arrayQuality/man/qualityScore.Rd
arrayQuality/man/readAgilent.Rd
arrayQuality/man/readGPR.Rd
arrayQuality/man/readSpikeTypes.Rd
arrayQuality/man/readSpot.Rd
arrayQuality/man/readcontrolCode.Rd
arrayQuality/man/scaleRefTable.Rd
arrayQuality/man/slideQuality.Rd
arrayQuality/man/spotQuality.Rd
arrayQuality/vignettes
arrayQuality/vignettes/basicQuality.html
arrayQuality/vignettes/customQuality.html
arrayQuality/vignettes/images
arrayQuality/vignettes/images/9mersDiagnosticPlot.png
arrayQuality/vignettes/images/QCHybDiagPlot.png
arrayQuality/vignettes/images/comparativeBoxplot.png
arrayQuality/vignettes/images/genHybDiagPlot.png
arrayQuality/vignettes/images/htmlReport.png
arrayQuality/vignettes/images/lifecycle.png
arrayQuality/vignettes/images/mySpotTypes.png
arrayQuality/vignettes/images/qualityDiagram.png
arrayQuality/vignettes/index.html
arrayQuality/vignettes/meeboQualityGuide.htm
arrayQuality/vignettes/meeboQualityGuide_files
arrayQuality/vignettes/meeboQualityGuide_files/filelist.xml
arrayQuality/vignettes/meeboQualityGuide_files/header.htm
arrayQuality/vignettes/meeboQualityGuide_files/image001.jpg
arrayQuality/vignettes/meeboQualityGuide_files/image003.jpg
arrayQuality/vignettes/meeboQualityGuide_files/image005.png
arrayQuality/vignettes/meeboQualityGuide_files/image007.png
arrayQuality/vignettes/meeboQualityGuide_files/image009.png
arrayQuality/vignettes/meeboQualityGuide_files/image011.png
arrayQuality/vignettes/meeboQualityGuide_files/image013.png
arrayQuality/vignettes/meeboQualityGuide_files/image015.png
arrayQuality/vignettes/meeboQualityGuide_files/image017.png
arrayQuality/vignettes/meeboQualityGuide_files/image019.png
arrayQuality/vignettes/meeboQualityGuide_files/image021.png
arrayQuality/vignettes/print-runQC.html