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

[James W. MacDonald]

michael driscoll wrote:
> hello,
> 
> 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.

One might argue that an ideal cdf package would eliminate 
cross-hybridizing probes so you could be sure that you are only 
interrogating one transcript per probeset.

We now have packages (cdf and probe) that do just that - supplied to us 
by the folks at the Molecular and Behavioral Neuroscience Institute at 
UMich. If you are interested, you can browse these packages using biocViews:

http://www.bioconductor.org/packages/1.8/AnnotationData.html

and more information can be found on the MBNI web page:

http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp

Best,

Jim


> 
> 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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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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