inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2.R

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

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

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# Setup
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dataSet <- "GSE8605"
chipType <- "Mapping10K_Xba142"
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType, verbose=verbose)
print(csR)



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# (a) CRMAv2
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res <- doCRMAv2(csR, drop=FALSE, verbose=verbose)
print(res)


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# (b) CRMAv2
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# Process only the first six arrays (and in reverse order)
subset <- c(2,5,3)
dsN <- doCRMAv2(csR, arrays=subset, verbose=verbose)
print(dsN)


# Sanity checks
# Assert same output as input arrays (in the same order)
sampleNames <- getNames(csR)[subset]
stopifnot(getNames(dsN) == sampleNames)



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# (c) CRMAv2
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# Process only the first six arrays (and in reverse order)
subset <- c(2,5,3)
dsN2 <- doCRMAv2(dataSet, chipType=chipType, arrays=subset, verbose=verbose)
print(dsN2)

# Sanity checks
stopifnot(equals(dsN2, dsN))