[BioC] probe alignment clustering

[Stan Smiley]

I'm in the process of validating the annotation from Affymetrix, and
positioning each 25mer probe
on the genome (just mouse and human so far). I'm in a position now to
use this
positioning data to validate the affy annotated alignments, which I'm
doing now.

My challenge now is to settle on the best approach in BioC/R to find
'consensus' sequences
in the genome that best match the alignments I've come up with. I'm
thinking some
clustering package, but not sure which one is most appropriate.

I searched the BioC archives but couldn't find anything on this subject.

Any direction on this would be greatly appreciated!


Thanks,

Stan Smiley