inst/testScripts/system/chipTypes/Mapping250K_Sty/22.doASCRMAv2,singleArray.R

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

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-4, timestamp=TRUE)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataSet <- "GSE12019,testset"
chipType <- "Mapping250K_Sty"

csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)



# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# (a) CRMAv2 - six arrays
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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=extract, 1)
for (key in names(dsNList1)) {
  print(key)
  dsN0 <- dsNList0[[key]]
  dsN1 <- dsNList1[[key]]
  stopifnot(getFullNames(dsN1) == getFullNames(dsN0))
  data0 <- extractMatrix(dsN0)
  data1 <- extractMatrix(dsN1)
  rho <- cor(data1, data0, use="complete.obs")
  print(rho)
  res <- all.equal(data1, data0)
  print(res)

  # Sanity check
  stopifnot(all.equal(data1, data0))
} # for (key ...)