inst/testScripts/robustness/chipTypes/MoGene-1_0-st-v1/11.GcRmaBgCorr.R

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

library("aroma.affymetrix")
verbose <- Arguments$getVerbose(-10, timestamp=TRUE)

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataSet <- "GSE37861"
chipType <- "MoGene-1_0-st-v1"

cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
print(cdf)

csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf)
csR <- csR[1:6]
print(csR)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# gcRMA-style background correction
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Currently, you must use the standard CDF file.
bc <- GcRmaBackgroundCorrection(csR, type="affinities")
print(bc)

# This should throw "Error: Cannot perform GCRMA background
# (type="affinities") correction: The number (0) of negative
# control is too small."
tryCatch({
  csB <- process(bc, verbose=verbose)
}, error = function(ex) {
  print(ex)
})