inst/testScripts/system/chipTypes/HG-U133_Plus_2/81.doRMA,extractExpressionSet.R

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

library("aroma.affymetrix")
library("Biobase")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)

dataSet <- "GSE9890"
chipType <- "HG-U133_Plus_2"
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)

ces <- doRMA(csR, verbose=verbose)
print(ces)

eset <- extractExpressionSet(ces, verbose=verbose)
print(eset)
print(sampleNames(eset))

# Sanity checks
stopifnot(identical(sampleNames(eset), getNames(ces)))
stopifnot(identical(featureNames(eset), getUnitNames(getCdf(ces))))


# Add 'annotation' slot
eset <- extractExpressionSet(ces, annotationPkg="PDInfo", verbose=verbose)
print(eset)
print(annotation(eset))
stopifnot(annotation(eset) == "pd.hg.u133.plus.2")

eset <- extractExpressionSet(ces, annotationPkg="cdf", verbose=verbose)
print(eset)
print(annotation(eset))
stopifnot(annotation(eset) == "hgu133plus2cdf")

eset <- extractExpressionSet(ces, annotationPkg="ChipDb", verbose=verbose)
print(eset)
print(annotation(eset))
stopifnot(annotation(eset) == "hgu133plus2")