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

[michael driscoll]

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