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

[lgautier at altern.org]

Whatever your reasons are for wanting a probe to concurrently appear
in different probe sets, this is indeed not handled by the package
altcdfenvs.

The idea was to contruct whatever mapping directly in R
(and skip the potentially painful procedure of creating CDF files,
just to see them read into R right after).

If you want to have probes appearing in several probe sets, I would wait
for after pre-processing data (background correction, normalization).

If you want to use your very own mapping (for reason that might
belong to your particular experimental setting -e.g., using a slightly
different species than the one the chip was designed against, or using
using it with a transgenic organism-, or supplementary knowledge
you might have), the package 'atltcdfenvs' will be your friend.
Tasks like removing cross-hybridizing probes will be easy (in that
case, a single call to the function "unique.CdfEnvAffy" will do the job).


Laurent


> 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.
>
> 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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