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

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

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)

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# Setup
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dataSet <- "GSE13372,testset"
chipType <- "GenomeWideSNP_6,Full"

csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)


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


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# Summarize theta = thetaA+thetaB
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cesN <- res$cesN
as <- AlleleSummation(cesN)
print(as)
cesT <- process(as, verbose=verbose)
print(cesT)

Y <- extractMatrix(cesT, verbose=verbose)
print(head(Y))


# Validation
dsNList <- res$dsNList
Y0 <- extractMatrix(dsNList$total, verbose=verbose)
print(head(Y0))

# Sanity check
stopifnot(all.equal(Y, Y0))


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# Segmentation
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cbs <- CbsModel(cesT)
print(cbs)

ce <- ChromosomeExplorer(cbs, zooms=2^(0:5))
process(ce, arrays=1:2, chromosomes=18:23, verbose=verbose)