Affymetrix expression data quality control and reproducibility analysis


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Documentation for package ‘yaqcaffy’ version 1.32.0

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arrays Class "YAQCStats"
arrays-method Class "YAQCStats"
avbg-method Class "YAQCStats"
avns Class "YAQCStats"
avns-method Class "YAQCStats"
bio Class "YaqcControlProbes"
bio-method Class "YaqcControlProbes"
bio-methods Class "YaqcControlProbes"
bioCalls Class "YAQCStats"
bioCalls-method Class "YAQCStats"
class:YaqcBioProbes Class "YaqcControlProbes"
class:YaqcControlProbes Class "YaqcControlProbes"
class:YaqcDegProbes Class "YaqcControlProbes"
class:YaqcSpkProbes Class "YaqcControlProbes"
class:YAQCStats Class "YAQCStats"
deg Class "YaqcControlProbes"
deg-method Class "YaqcControlProbes"
deg-methods Class "YaqcControlProbes"
gcosProbes Class "YAQCStats"
gcosProbes-method 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 Class "YAQCStats"
getYaqcControlProbes-method Class "YAQCStats"
info Class "YaqcControlProbes"
info-method Class "YaqcControlProbes"
info<- Class "YaqcControlProbes"
info<--method Class "YaqcControlProbes"
isLog Class "YAQCStats"
isLog-method Class "YAQCStats"
merge-method Class "YAQCStats"
method:yaqc 'YAQCStats' constructor
minbg-method Class "YAQCStats"
moreSpikeInProbes Class "YAQCStats"
moreSpikeInProbes-method Class "YAQCStats"
objectVersion Class "YAQCStats"
objectVersion-method Class "YAQCStats"
percent.present-method Class "YAQCStats"
plot,YAQCStats Plots a YAQCStats object
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
sfs-method Class "YAQCStats"
show-method Class "YAQCStats"
show-method Class "YaqcControlProbes"
spk Class "YaqcControlProbes"
spk-method Class "YaqcControlProbes"
spk-methods Class "YaqcControlProbes"
summary-method Class "YAQCStats"
target-method Class "YAQCStats"
yaqc 'YAQCStats' constructor
yaqc-method 'YAQCStats' constructor
yaqc-methods 'YAQCStats' constructor
yaqc.affy 'YAQCStats' constructor
yaqc.plot Plots a YAQCStats object
yaqc.summary Class "YAQCStats"
YaqcBioProbes-class Class "YaqcControlProbes"
YaqcControlProbes-class Class "YaqcControlProbes"
YaqcDegProbes-class Class "YaqcControlProbes"
YaqcSpkProbes-class Class "YaqcControlProbes"
YAQCStats-class Class "YAQCStats"