inst/testScripts/system/chipTypes/MoGene-1_0-st-v1/12.QuantileNormalization.R

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

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

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# Setup data set
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dataSet <- "GSE37861"
chipType <- "MoGene-1_0-st-v1"

cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
print(cdf)

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


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# RMA background correction
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# Currently, you must use the standard CDF file.
bc <- RmaBackgroundCorrection(csR)
print(bc)

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


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# Quantile normalization
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qn <- QuantileNormalization(csB, typesToUpdate="pm")
csN <- process(qn, verbose=verbose)
print(csN)