First, I am very new to this and have been learning a lot in a 3 week crash
course involvement a project. My point is that I am not great with the
terminology.

What I have, ~50 affycel files, and 3 groups of ~8 samples each for which I
know the genome for, ie I know what probes/sequences should bind. We do not
have a CDF file as this is a custom array with a mix of probe purposes.
Basically these 3 groups of 8 are my means of validating the method used

The other ~25 are unknown and I would like a to put a probability on each
probe/sequence of the likelihood that a sequence that matches. ie is in the
genome. of the unknown.

I also have single snp mismatch data for each of the known and the location
of the mismatch in the sequence.


Are there any tools in bioconductor and or methods that I should look at. Up
to this point I have been using python to merge the different data and do
some initial analysis.


  *Vincent Davis
720-301-3003 *
vincent@vincentdavis.net
 my blog <http://vincentdavis.net> |
LinkedIn<http://www.linkedin.com/in/vincentdavis>

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