library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataSet <- "GSE13372,testset"
chipType <- "GenomeWideSNP_6,Full"
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# (a) AS-CRMAv2
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dsNList <- doASCRMAv2(csR, verbose=verbose)
print(dsNList)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# (b) CRMAv2 - single array
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup a single array
csR1 <- csR[1]
# Rename data set in order to not pick up existing results
setFullName(csR1, sprintf("%s,singleArray", getFullName(csR1)))
dsNList1 <- doASCRMAv2(csR1, verbose=verbose)
print(dsNList1)
# Sanity checks
dsNList0 <- lapply(dsNList, FUN=`[`, 1)
for (key in names(dsNList1)) {
verbose && enter(verbose, key)
dsN0 <- dsNList0[[key]]
verbose && print(verbose, dsN0)
dsN1 <- dsNList1[[key]]
verbose && print(verbose, dsN1)
stopifnot(getFullNames(dsN1) == getFullNames(dsN0))
data0 <- extractMatrix(dsN0)
data1 <- extractMatrix(dsN1)
rho <- cor(data1, data0, use="complete.obs")
verbose && print(verbose, rho)
res <- all.equal(data1, data0)
verbose && print(verbose, res)
# Sanity check
stopifnot(all.equal(data1, data0))
verbose && exit(verbose)
} # for (key ...)
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