Affymetrix expression data quality control and reproducibility analysis


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Documentation for package ‘yaqcaffy’ version 1.2.0

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arrays Accessor Methods for YAQCStats class
arrays,YAQCStats-method Class "YAQCStats"
arrays-methods Class "YAQCStats"
avns Accessor Methods for YAQCStats class
avns,YAQCStats-method Class "YAQCStats"
avns-methods Class "YAQCStats"
bioCalls Accessor Methods for YAQCStats class
bioCalls,YAQCStats-method Class "YAQCStats"
bioCalls-methods Class "YAQCStats"
gcosProbes Accessor Methods for YAQCStats class
gcosProbes,YAQCStats-method Class "YAQCStats"
gcosProbes-methods Class "YAQCStats"
getAllInt Get the GCOS 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
isLog Accessor Methods for YAQCStats class
isLog,YAQCStats-method Class "YAQCStats"
isLog-methods Class "YAQCStats"
merge,YAQCStats-method Class "YAQCStats"
moreSpikeInProbes Accessor Methods for YAQCStats class
moreSpikeInProbes,YAQCStats-method Class "YAQCStats"
moreSpikeInProbes-methods Class "YAQCStats"
morespikes The name of more spike probes
plot Accessor Methods for YAQCStats class
plot,YAQCStats Plots a YAQCStats object
plot,YAQCStats,ANY-method Class "YAQCStats"
plot,YAQCStats,missing-method Plots a YAQCStats object
plot,YAQCStats-method Plots a YAQCStats object
reprodPlot Plot human whole genome GeneChips reproductibility
show,YAQCStats-method Class "YAQCStats"
target,YAQCStats-method Class "YAQCStats"
target-methods Class "YAQCStats"
yaqc Generate QC stats from an AffyBatch object
yaqc,eSet-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
YAQCStats-class Class "YAQCStats"