[BioC] Affymetrix SDK Bioconductor package?

[James Bullard]

Hi all, we have been working for the last month or so on integrating the 
Affymetrix parsing SDK 2.0 into an R package. We began because we had a 
CDF file which would not parse with the existing libraries in 
Bioconductor (the problem turned out to be in the CDF file itself). In 
any case, we have spent a good amount of time on providing an interface 
to this package in R, specifically duplicating the interfaces which are 
currently available in Bioconductor to the CDF, CEL, CHP, BPMAP, and BAR 
files (where relevant). One of the nice things about the library is that 
binary formats are also accepted so the same interface can parse both 
text and binary transparently. Also, it should be much easier to absorb 
new library changes when Affymetrix releases new SDKs and file formats.

The library still needs some work, but before I spend a *lot* more time 
on it I wanted to know 1.) if people thought this would be good thing to 
have and 2.) if someone was already working on integrating these libraries.

We are hopeful that people will think this is a good idea - we cannot 
see any reason why this would not be a good addition to Bioconductor, 
and would very much like to finish the work with the blessing of the 
BioC community.

Thanks, jim

-- 
James Bullard
bullard at berkeley.edu
760.267.0986