inst/testScripts/system/chipTypes/HuEx-1_0-st-v2/test20101202,gcrma.R

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

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-3, timestamp=TRUE)


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# Setup data set
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dataSet <- "Affymetrix-HeartBrain"
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR3,A20071112,EP")
print(cdf)

# Setup CEL set using the core CDF.
csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)


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# Process only cerebellum and heart
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types <- c("cerebellum", "heart")
csR <- csR[indexOf(csR, patterns=types)]

setFullName(csR, sprintf("%s,%s", dataSet, paste(types, collapse="+")))
print(csR)


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# Background correction and normalization
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cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
setCdf(csR, cdfS)
bc <- GcRmaBackgroundCorrection(csR, type="affinities")
print(bc)

csB <- process(bc, verbose=verbose)
print(csB)
setCdf(csB, cdf)