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

Mario Caceres wrote: > 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. I would strongly dissuade one to play with the CDF file directly, but rather work at the level of the CDF environment. The package altcdfenvs was designed for these tasks. > 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. This should be fairly easy to do. See if the following vignette int the package altcdfenvs helps you to see how to do it for your data: http://www.bioconductor.org/repository/devel/vignette/ngenomeschips.pd f > Any help would be greatly appreciated! Hoping it helps, Laurent > Thanks, > > Mario > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >