inst/testScripts/complete/dataSets/GSE34754/22.doASCRMAv2,CalMaTe.R

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

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# Allele-specific CRMAv2
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future::plan("multisession")
library("aroma.affymetrix")
library("calmate")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)


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# Setup
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dataSet <- "GSE34754"
chipType <- "Mapping250K_Nsp"

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


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# AS-CRMAv2
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dsNList <- doASCRMAv2(csR, verbose=verbose)
print(dsNList)

dsN <- exportAromaUnitPscnBinarySet(dsNList)
print(dsN)


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# CalMaTe
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cmt <- CalMaTeCalibration(dsNList)
print(cmt)

dsCList <- process(cmt, verbose=verbose)
print(dsCList)

dsC <- exportAromaUnitPscnBinarySet(dsCList)
print(dsC)