yaqcaffy: Affymetrix expression data quality control and reproducibility analysis
Version 1.36.0

Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

Browse man pages Browse package API and functions Browse package files

AuthorLaurent Gatto
Bioconductor views Microarray OneChannel QualityControl ReportWriting
Date of publicationNone
MaintainerLaurent Gatto <lg390@cam.ac.uk>
LicenseArtistic-2.0
Version1.36.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("yaqcaffy")

Man pages

getAllInt: Get the summerized MAS5 values for a given spike probe
getBioProbes: Get the names of the Bio spike probes on the array
getOutliers: Get outliers for the different YAQCStatsObject slots
getQCRatios: Compute qc probe ratios using GCOS intensity values
getRatioProbes: Get the names of degradation control probes on the array
getSpikeProbes: Get the names of all spike probes on the array
probeSelectionInterface: Tcltk Interface to Generate an Instance of YaqcControlProbes...
reprodPlot: Plot human whole genome GeneChips reproductibility
yaqc.affy: 'YAQCStats' constructor
YaqcControlProbes-class: Class "YaqcControlProbes"
yaqc.plot: Plots a YAQCStats object
YAQCStats-class: Class "YAQCStats"

Functions

YAQCStats-class Man page
YaqcBioProbes-class Man page
YaqcControlProbes-class Man page
YaqcDegProbes-class Man page
YaqcSpkProbes-class Man page
arrays Man page
arrays,YAQCStats-method Man page
avbg,YAQCStats-method Man page
avns Man page
avns,YAQCStats-method Man page
bcalls Source code
bio Man page
bio,YaqcBioProbes-method Man page
bio,YaqcControlProbes-method Man page
bio-methods Man page
bioCalls Man page
bioCalls,YAQCStats-method Man page
checkNumberOfProbes Source code
class:YAQCStats Man page
class:YaqcBioProbes Man page
class:YaqcControlProbes Man page
class:YaqcDegProbes Man page
class:YaqcSpkProbes Man page
deg Man page
deg,YaqcControlProbes-method Man page
deg,YaqcDegProbes-method Man page
deg-methods Man page
gcosProbes Man page
gcosProbes,YAQCStats-method Man page
getAllInt Man page Source code
getAlpha1 Source code
getAlpha2 Source code
getBio Source code
getBioProbes Man page Source code
getDeg Source code
getOutliers Man page Source code
getQCRatios Man page Source code
getQcdefData Source code
getRatioProbes Man page Source code
getSpikeProbes Man page Source code
getSpk Source code
getSpkProbes Source code
getYaqcControlProbes Man page Man page
getYaqcControlProbes,YAQCStats-method Man page Man page
info Man page
info,YaqcControlProbes-method Man page
info<- Man page
info<-,YaqcControlProbes-method Man page
isLog Man page
isLog,YAQCStats-method Man page
merge,YAQCStats,YAQCStats-method Man page
merge,YAQCStats-method Man page
merge.yaqc Source code
mergeAffyBatchObjects Source code
method:yaqc Man page
minbg,YAQCStats-method Man page
moreSpikeInProbes Man page
moreSpikeInProbes,YAQCStats-method Man page
objectVersion Man page
objectVersion,YAQCStats-method Man page Man page
percent.present,YAQCStats-method Man page
plot,YAQCStats Man page
plot,YAQCStats,missing-method Man page
plotAvbg Source code
plotAvns Source code
plotBioQC Source code
plotPp Source code
plotQCRatios Source code
plotSfs Source code
plotSpikesQC Source code
plotdata Source code
plotdiag Source code
plotrectangle Source code
probeSelectionInterface Man page Source code
removeOK Source code
reprodPlot Man page Source code
sHgu133plus2 Source code
sfs,YAQCStats-method Man page
show,YAQCStats-method Man page
show,YaqcBioProbes-method Man page
show,YaqcControlProbes-method Man page
show,YaqcDegProbes-method Man page
show,YaqcSpkProbes-method Man page
spk Man page
spk,YaqcControlProbes-method Man page
spk,YaqcSpkProbes-method Man page
spk-methods Man page
summary,YAQCStats-method Man page
target,YAQCStats-method Man page
yaqc Man page
yaqc,AffyBatch-method Man page
yaqc,ExpressionSet-method Man page
yaqc,eSet-method Man page
yaqc-method Man page
yaqc-methods Man page
yaqc.affy Man page Source code
yaqc.affy.affybatch Source code
yaqc.affy.exprSet Source code
yaqc.plot Man page Source code
yaqc.plot.all Source code
yaqc.plot.part Source code
yaqc.show Source code
yaqc.summary Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllGenerics.R
R/DataClasses.R
R/getControlProbes.R
R/probeSelectionInterface.R
R/reprod.R
R/yaqc.plots.R
R/yaqc.stats.R
R/yaqcCtrlProbes.R
TODO
build
build/vignette.rds
inst
inst/doc
inst/doc/yaqcaffy.R
inst/doc/yaqcaffy.Rnw
inst/doc/yaqcaffy.pdf
man
man/YAQCStats-class.Rd
man/YaqcControlProbes-class.Rd
man/getAllInt.Rd
man/getBioProbes.Rd
man/getOutliers.Rd
man/getQCRatios.Rd
man/getRatioProbes.Rd
man/getSpikeProbes.Rd
man/probeSelectionInterface.Rd
man/reprodPlot.Rd
man/yaqc.affy.Rd
man/yaqc.plot.Rd
vignettes
vignettes/Screenshot-Filtered_selection.png
vignettes/yaqcaffy.Rnw
yaqcaffy documentation built on May 20, 2017, 9:23 p.m.