inst/testScripts/system/chipTypes/MoEx-1_0-st-v1/11.GcRmaBackgroundCorrection.R

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

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-10, timestamp=TRUE)


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# Setup
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dataSet <- "GSE20403"
chipType <- "MoEx-1_0-st-v1"

cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR1,A20080718,MR")
print(cdf)

csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
csR <- csR[1:6]
print(csR)


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# gcRMA-style background correction
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# Currently, you must use the standard CDF file.
cdf <- getCdf(csR)
cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
setCdf(csR, cdfS)
bc <- GcRmaBackgroundCorrection(csR, type="affinities")
print(bc)
csB <- process(bc, verbose=verbose)
print(csB)
# Now, use the custom CDF in what follows
setCdf(csB, cdf)
print(csB)