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

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

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-50, 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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# GC-content normalization
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cesN <- res$cesN
gcn <- GcContentNormalization2(cesN, target="zero")
print(gcn)
cesN2 <- process(gcn, verbose=verbose)
print(cesN2)


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# GC-content effects before and after normalization
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cdf <- getCdf(cesN)
ugp <- getAromaUgpFile(cdf)
units <- getUnitsOnChromosomes(ugp, 1:22)

# Down sample
units <- units[seq(from=1, to=length(units), by=4)]

# Before
toPNG(getFullName(gcn), tags=c("BeforeGCN"), {
  par(mar=c(4,3,1,1)+0.1, mgp=c(2.0,0.7,0))
  plotCovariateEffects(gcn, units=units, ylim=c(0,16), verbose=verbose)
})

# After
toPNG(getFullName(gcn), tags=c("AfterGCN"), {
  par(mar=c(4,3,1,1)+0.1, mgp=c(2.0,0.7,0))
  gcn2 <- GcContentNormalization2(cesN2, target="zero")
  plotCovariateEffects(gcn2, units=units, ylim=c(0,16), verbose=verbose)
})