arrayQuality: Assessing array quality on spotted arrays
Version 1.54.0

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

Browse man pages Browse package API and functions Browse package files

AuthorAgnes Paquet and Jean Yee Hwa Yang <yeehwa@stat.berkeley.edu>
Bioconductor views Microarray QualityControl TwoChannel Visualization
Date of publicationNone
MaintainerAgnes Paquet <paquetagnes@yahoo.com>
LicenseLGPL
Version1.54.0
URL http://arrays.ucsf.edu/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("arrayQuality")

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...

Functions

12Mm250.gpr Man page
9Mm137.gpr Man page
BEbin.linear Man page Source code
EMSplit Man page Source code
HeeboSpotTypes Man page
HsReferenceDB Man page
MeeboSpotTypes Man page
MmDEGenes Man page
MmReferenceDB Man page
PRv9mers Man page Source code
PRvQCHyb Man page Source code
Spike.Cy5vsCy3 Man page Source code
Spike.Individual.Sensitivity Man page Source code
Spike.MM.Scatter Man page Source code
Spike.MMplot Man page Source code
Spike.Sensitivity Man page Source code
agQuality Man page Source code
agcontrolCode Man page
arrayControls Man page Source code
arrayReplicates Man page Source code
arrayScal Man page Source code
controlCodeHeebo Man page
controlCodeMeebo Man page
getSpikeIds Man page Source code
getSpikeIndex Man page Source code
globalQuality Man page Source code
gpFlagWt Man page Source code
gpQuality Man page Source code
heeboQuality Man page Source code
heeboQualityPlots Man page Source code
index.html Man page
maQualityPlots Man page Source code
meeboQuality Man page Source code
meeboQualityPlots Man page Source code
outputNormData Man page Source code
qcScore Man page Source code
qpBEplot.linear Man page Source code
qpBoxplotMeebo Man page Source code
qpDotPlots Man page Source code
qpDotPlotsEEBO Man page Source code
qpDotPlotsMeebo Man page Source code
qpDotPlotsMeebo2 Man page
qpHexbin Man page Source code Source code Source code
qpImage Man page Source code
qpMAPlots Man page Source code
qpMisMatchPlot Man page Source code
qpPTLoess Man page Source code
qpS2N Man page Source code
qpS2Neebo Man page Source code
qpS2Nmeebo Man page Source code
qpTiling Man page Source code
qualBoxplot Man page Source code
quality2HTML Man page Source code
qualityScore Man page Source code
readAgilent Man page Source code
readAllSpikes Man page Source code
readGPR Man page Source code
readSpikeTypes Man page Source code
readSpot Man page Source code
readcontrolCode Man page Source code
replicatesAvariance Man page Source code
scaleRefTable Man page Source code
setCtlCol Man page Source code
slideQuality Man page Source code
spotQuality Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/PRQCv1.R
R/PRQCv2.R
R/agQuality.R
R/arrayControl.R
R/gpQuality.R
R/heeboQuality.R
R/heeboSetQC.R
R/meeboQuality.R
R/qpHeeboFunc.R
R/qpHexbin.R
R/qpMeeboFunc.R
R/qualFunc.R
R/qualityPlots.R
R/spikeIn.R
R/spotQuality.R
data
data/HsReferenceDB.RData
data/MmDEGenes.RData
data/MmReferenceDB.RData
inst
inst/Heebo
inst/Heebo/63421.gpr
inst/Heebo/DCV2.0June06.txt
inst/Heebo/hoc.gal
inst/Meebo
inst/Meebo/MeeboSpotType.txt
inst/Meebo/RDI108_n.gpr
inst/Meebo/StanfordDCV1.7complete.txt
inst/gprQCData
inst/gprQCData/12Mm250.gpr
inst/gprQCData/9Mm137.gpr
inst/gprQCData/index.html
man
man/MmDEGenes.Rd
man/PRv9mers.Rd
man/PRvQCHyb.Rd
man/agQuality.Rd
man/arrayQuality-internal.Rd
man/globalQuality.Rd
man/gpQuality.Rd
man/gprDB.Rd
man/heeboQuality.Rd
man/heeboQualityPlots.Rd
man/maQualityPlots.Rd
man/meeboQuality.Rd
man/meeboQualityPlots.Rd
man/prdata.Rd
man/qcScore.Rd
man/qualBoxplot.Rd
man/qualityScore.Rd
man/readAgilent.Rd
man/readGPR.Rd
man/readSpikeTypes.Rd
man/readSpot.Rd
man/readcontrolCode.Rd
man/scaleRefTable.Rd
man/slideQuality.Rd
man/spotQuality.Rd
vignettes
vignettes/basicQuality.html
vignettes/customQuality.html
vignettes/images
vignettes/images/9mersDiagnosticPlot.png
vignettes/images/QCHybDiagPlot.png
vignettes/images/comparativeBoxplot.png
vignettes/images/genHybDiagPlot.png
vignettes/images/htmlReport.png
vignettes/images/lifecycle.png
vignettes/images/mySpotTypes.png
vignettes/images/qualityDiagram.png
vignettes/index.html
vignettes/meeboQualityGuide.htm
vignettes/meeboQualityGuide_files
vignettes/meeboQualityGuide_files/filelist.xml
vignettes/meeboQualityGuide_files/header.htm
vignettes/meeboQualityGuide_files/image001.jpg
vignettes/meeboQualityGuide_files/image003.jpg
vignettes/meeboQualityGuide_files/image005.png
vignettes/meeboQualityGuide_files/image007.png
vignettes/meeboQualityGuide_files/image009.png
vignettes/meeboQualityGuide_files/image011.png
vignettes/meeboQualityGuide_files/image013.png
vignettes/meeboQualityGuide_files/image015.png
vignettes/meeboQualityGuide_files/image017.png
vignettes/meeboQualityGuide_files/image019.png
vignettes/meeboQualityGuide_files/image021.png
vignettes/print-runQC.html
arrayQuality documentation built on May 20, 2017, 9:23 p.m.