Nothing
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")
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