inst/testScripts/robustness/chipTypes/Mapping50K_Hind240/21.doASCRMAv2,CRLMM.R

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

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

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataSet <- "HapMap,CEU,testset"
chipType <- "Mapping50K_Hind240"

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


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# AS-CRMAv2
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
res <- doASCRMAv2(csR, drop=FALSE, verbose=verbose)
print(res)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CRLMM
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ces <- res$cesN
print(ces)

# This should throw "Exception: Cannot fit CRLMM model: CRLMM 
# requires that the probe-level model was fitted without
# merging the strands (mergeStrands=FALSE)."
tryCatch({
  crlmm <- CrlmmModel(ces, tags="*,oligo", recalibrate=TRUE)
}, error = function(ex) {
  print(ex)
})