I have some CEL files and a CDF file for them, now how I can remove Control probesets (probesets with name started by AFFX) please? I mean how I can define these probesets to enter them in text file to be excluded without need to R?
Hi Sarah, CEL files are binary files, so they will not be readable in a text editor -- you will have to use R or Matlab. Is there any reason in particular you do not want to use R?
Once they are loaded into R, it shouldn't be too difficult to remove them; given all of them have the standardised format of starting with "AFFX", you can use grep:
# load the affy library
# read CEL files in your working directory and normalise them
data <- ReadAffy()
exp <- rma(data)
# remove all probes starting with "AFFX"
control <- grep("AFFX",rownames(exp))
exp <- exp[-control,]