[BioC] Making alternative CDF enviroments

[Mario Caceres]

Hello all,
 
I am trying to reanalyze some published Affymetrix human and chimpanzee data eliminating the probes that include sequence differences between the two species. I think I have finally figured out that I need to create an alternative CDF file and CDF enviroment for the unconventional chip with the new definitions of the probes sets. However, I am not sure of which is the best way to proceed or if there is already some tool in the Bioconductor package that will allow me to do that easily. I basically have a list of 50,000 probes that I would like to remove from the analysis.
 
Any help would be greatly appreciated!
 
Thanks,
 
Mario