[BioC] probe --> probe set mapping in CDF library files

[Wolfgang Huber]

Hi Michael,

it should be straightforward to prepare a CDF environment as you 
describe from your own probe-transcriptome alignment, and afaIk most (or 
all) functions in the affy package etc would work.

However, why would you want to do this? If anything, I'd have thought 
one wants to exclude probes that have multiple matches, rather than have 
them sit around in (and contaminate) multiple places. If a probe hits 
multiple places in the genome, this is in almost all cases not sporadic, 
but because the hit regions share a common ancestor.

Best wishes
  Wolfgang

> 
> i'm a researcher at Boston U. and a user of Bioconductor.
> 
> currently, Affymetrix-provided CDF library files associate each probe
> with a single probe set -- a one-to-one mapping -- even when that
> probe is known to cross-hybridize to other probe sets (or more
> precisely, when that probe cross-hybrizes to other regions of sequence
> targeted by other probe sets).
> 
> an ideal CDF library file would have a one-to-many mapping of a probe
> to probe sets.  in an actual CDF file, this would mean that a probe's
> x,y coordinates and description line would be listed in multiple unit
> blocks -- instead of just once.
> 
> would such a file work with existing Bioconductor packages?  does the
> current implementation require a single association of probe--> probe
> sets?
> 
> i have looked through Laurent Gautier's altcdfenvs package but have
> not found whether such a re-mapping would be possible.
> 
> any insights would be much appreciated.
> 
> sincerely, mike
> ___________________
> michael driscoll
> bioinformatics program
> boston university
> http://www.bu.edu/abl
> http://gardnerlab.bu.edu
> 
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-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber