[BioC] Using a custom CDF file

[Nathan Haigh]

I'm using the xspecies [1] approach of hybridising gDNA to the Affy ATH1
chip. Using these, one masks out low intensity probes and creates a new
CDF file - this is done several times using a different intensity
threshold. I then want to analyse RNA hybs to the ATH1 chip using each
of these different CDF files.

Is it possible, for example, to tell ReadAffy() to use a certain CDF
file? If so, I could write a nice R script to do all the processing etc.
Or do I have to make a CDF package? If so, how/when do I specify the CDF
file to use?

I'm new to R/Bioconductor, so would appreciate any help towards this.

Cheers
Nathan

[1] http://affymetrix.arabidopsis.info/xspecies/