yaqcaffy: Affymetrix expression data quality control and reproducibility analysis

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

Author
Laurent Gatto
Date of publication
None
Maintainer
Laurent Gatto <lg390@cam.ac.uk>
License
Artistic-2.0
Version
1.34.0

View on Bioconductor

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"

Files in this package

yaqcaffy/DESCRIPTION
yaqcaffy/NAMESPACE
yaqcaffy/NEWS
yaqcaffy/R
yaqcaffy/R/AllGenerics.R
yaqcaffy/R/DataClasses.R
yaqcaffy/R/getControlProbes.R
yaqcaffy/R/probeSelectionInterface.R
yaqcaffy/R/reprod.R
yaqcaffy/R/yaqc.plots.R
yaqcaffy/R/yaqc.stats.R
yaqcaffy/R/yaqcCtrlProbes.R
yaqcaffy/TODO
yaqcaffy/build
yaqcaffy/build/vignette.rds
yaqcaffy/inst
yaqcaffy/inst/doc
yaqcaffy/inst/doc/yaqcaffy.R
yaqcaffy/inst/doc/yaqcaffy.Rnw
yaqcaffy/inst/doc/yaqcaffy.pdf
yaqcaffy/man
yaqcaffy/man/YAQCStats-class.Rd
yaqcaffy/man/YaqcControlProbes-class.Rd
yaqcaffy/man/getAllInt.Rd
yaqcaffy/man/getBioProbes.Rd
yaqcaffy/man/getOutliers.Rd
yaqcaffy/man/getQCRatios.Rd
yaqcaffy/man/getRatioProbes.Rd
yaqcaffy/man/getSpikeProbes.Rd
yaqcaffy/man/probeSelectionInterface.Rd
yaqcaffy/man/reprodPlot.Rd
yaqcaffy/man/yaqc.affy.Rd
yaqcaffy/man/yaqc.plot.Rd
yaqcaffy/vignettes
yaqcaffy/vignettes/Screenshot-Filtered_selection.png
yaqcaffy/vignettes/yaqcaffy.Rnw