[BioC] Affymetrix SDK Bioconductor package?

Kasper Daniel Hansen k.hansen at biostat.ku.dk
Wed Jun 1 21:55:22 CEST 2005

Is there really no-one who thinks it is a good idea to integrate the 
Affymetrix SDK for reading various file formats, into Bioconductor?


On Sat, May 21, 2005 at 10:58:19AM -0700, James Bullard wrote:
> 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
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Kasper Daniel Hansen, Research Assistant
Department of Biostatistics, University of Copenhagen

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