Using Custom Cdfs In R
I would like to use justRMA() in R/bioconductor using a remapped affymetrix CDF for u133a and u133aplus2.0 chips. I'd like to figure out how to ensure that I get an annotated expression set as I would using the affymetrix CDFs.
Thanks for your help.
Do you mean you don't want to use the existing Bioconductor packages, you want to build one from your own custom CDF file? If so, then maybe
You can browse the latest release versions of the CDF files
To install the latest release CDF for affy 133 a plus2.0:
I think the affy package will go out and get the latest CDF for you if you don't have one installed already.
MBNI's CDF might be an easy entry point to the world of remapped CDFs for Affymetrix.
The use of alternative probe-probeset mappings was mentioned in the
answer to an other question.
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