[BioC] gc-rma and vsn normalization for rat microarray data

Rainer Tischler rainer_t62 at yahoo.de
Fri Jun 11 17:20:32 CEST 2010

Dear all,

I am analyzing microarray data from an Affymetrix GeneChip Rat ST 1.0 platform, however, since there is no annotation package available that is compatible with the R-package "affy", so far I have only been able to normalize the data using the simple RMA method from the oligo-package. I would like to apply more advanced normalization methods like GC-RMA, VSN, PUMA or BGX, but none of these methods seems to be compatible with the oligo-package.
Is anybody aware of a possibility to analyze Affymetrix Rat data with the standard affy-package, or alternatively, a possibility to use any of the above normalization methods with the oligo-package?

Many thanks,

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