Someone in the lab is working on human xenogrefs in mouse, and wants to check expression of genes in the transplanted human cells. He asked me to find all the human probes from the affymetrix chip that are matching mouse transcripts. I got that list of probes and probesets, and liked to have a file selecting human specific probes. Something similar to what Naef et al. did in Nuc. Acids Res. (2005) vol.33 e111. They used their modified list of probes by modifying cdf files. Is there another easiest mean to do that ?

Personally, I would use Affymetrix Power Tools to generate the rma.summary.txt file. After, you could extract your probeset from this file by using R.

Thanks; I'll try that.

I agree; it's much easier to filter probes after processing CEL files than to try messing around with custom CDF files.