inst/testScripts/system/chipTypes/Mapping10K_Xba142/21.doCRMAv2,CBS,any.R

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

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

dataSet <- "GSE8605"
chipType <- "Mapping10K_Xba142"
res <- doCRMAv2(dataSet, chipType=chipType, drop=FALSE, verbose=verbose)
print(res)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CBS on a CnChipEffectSet
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cesN <- res$cesN
segA <- CbsModel(cesN, tags="*,cesN")
print(segA)

# Try to segment
fit(segA, arrays=1:2, chromosomes=19, verbose=verbose)

# Write to file
pathnameA <- writeRegions(segA, arrays=1:2, chromosomes=19, skip=FALSE, verbose=verbose)
print(pathnameA)

segTableA <- read.table(pathnameA, header=TRUE)
print(segTableA)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# CBS on an AromaUnitTotalCnBinarySet
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dsNList <- res$dsNList
dsT <- dsNList; # Hmm... should this have a different name?
segB <- CbsModel(dsT)
print(segB)

# Try to segment
fit(segB, arrays=1:2, chromosomes=19, verbose=verbose)

# Write to file
pathnameB <- writeRegions(segB, arrays=1:2, chromosomes=19, skip=FALSE, verbose=verbose)
print(pathnameB)

segTableB <- read.table(pathnameB, header=TRUE)
print(segTableB)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Compare
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Sanity check
stopifnot(all.equal(segTableB, segTableA))