Affymetrix expression data quality control and reproducibility analysis

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Documentation for package ‘yaqcaffy’ version 1.10.1

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arrays Accessor Methods for YAQCStats class
arrays-method Class "YAQCStats"
arrays-methods Class "YAQCStats"
avns Accessor Methods for YAQCStats class
avns-method Class "YAQCStats"
avns-methods Class "YAQCStats"
bio Class "YaqcControlProbes"
bio-method Class "YaqcControlProbes"
bio-methods Returns the 'bio' hybridization probes of YaqcControlProbes or YaqcBioProbes objects.
bioCalls Accessor Methods for YAQCStats class
bioCalls-method Class "YAQCStats"
bioCalls-methods Class "YAQCStats"
deg Class "YaqcControlProbes"
deg-method Class "YaqcControlProbes"
deg-methods Returns the degradation probes of YaqcControlProbes or YaqcDegProbes objects.
gcosProbes Accessor Methods for YAQCStats class
gcosProbes-method Class "YAQCStats"
gcosProbes-methods Class "YAQCStats"
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
getYaqcControlProbes Accessor Methods for YAQCStats class
getYaqcControlProbes,method Class "YAQCStats"
getYaqcControlProbes-method Class "YAQCStats"
info Class "YaqcControlProbes"
info-method Class "YaqcControlProbes"
info<- Class "YaqcControlProbes"
info<--method Class "YaqcControlProbes"
isLog Accessor Methods for YAQCStats class
isLog-method Class "YAQCStats"
isLog-methods Class "YAQCStats"
merge-method Class "YAQCStats"
moreSpikeInProbes Accessor Methods for YAQCStats class
moreSpikeInProbes-method Class "YAQCStats"
moreSpikeInProbes-methods Class "YAQCStats"
objectVersion Accessor Methods for YAQCStats class
objectVersion,method Class "YAQCStats"
objectVersion-method Class "YAQCStats"
plot Accessor Methods for YAQCStats class
plot,YAQCStats Plots a YAQCStats object
plot-method Class "YAQCStats"
plot-method Plots a YAQCStats object
probeSelectionInterface Tcltk Interface to Generate an Instance of YaqcControlProbes for a given Chip Set
reprodPlot Plot human whole genome GeneChips reproductibility
show-method Class "YAQCStats"
show-method Class "YaqcControlProbes"
spk Class "YaqcControlProbes"
spk-method Class "YaqcControlProbes"
spk-methods Returns the labelling probes of YaqcControlProbes or YaqcSpkProbes objects.
summary,YAQCStats Summarizes YAQCStats object outliers
summary-method Class "YAQCStats"
summary-method Summarizes YAQCStats object outliers
target-method Class "YAQCStats"
target-methods Class "YAQCStats"
yaqc Generate QC Stats from an AffyBatch Object
yaqc-method Create an YAQCStat object
yaqc-methods Create an YAQCStat object
yaqc.affy Generate QC Stats from an AffyBatch Object
yaqc.plot Plots a YAQCStats object
yaqc.summary Summarizes YAQCStats object outliers
YaqcBioProbes-class Class "YaqcControlProbes"
YaqcControlProbes-class Class "YaqcControlProbes"
YaqcDegProbes-class Class "YaqcControlProbes"
YaqcSpkProbes-class Class "YaqcControlProbes"
YAQCStats-class Class "YAQCStats"