[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
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
Kasper Daniel Hansen, Research Assistant
Department of Biostatistics, University of Copenhagen
More information about the Bioconductor