inst/testScripts/system/chipTypes/GenomeWideSNP_6/21.doASCRMAv2,plotACC.R

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-4, timestamp=TRUE)

dataSet <- "GSE13372,testset"
chipType <- "GenomeWideSNP_6,Full"
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# AS-CRMAv2
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
res <- doASCRMAv2(csR, drop=FALSE, verbose=verbose)
print(res)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Plot allele pairs before and after calibration
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
acc <- res$acc
for (what in c("input", "output")) {
  toPNG(getFullName(acc), tags=c("allelePairs", what), aspectRatio=0.7, {
    plotAllelePairs(acc, array=1, what=what, verbose=verbose)
  })
}