inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/51.ACC,merge.R

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

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


dataSet <- "HapMap,CEU,testset"
chipType <- "Mapping50K_Hind240"


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Tests for setting up CEL sets and locating the CDF file
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
print(csR)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Allelic cross-talk calibration
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
acc <- AllelicCrosstalkCalibration(csR, mergeShifts=FALSE)
print(acc)
csC <- process(acc, verbose=log)
print(csC)