Hi Elai,
Currently we are using the Affymetrix CDF to create our custom cdfs. You
think of the custom cdfs as reshuffling and trimming the information
that is on that cdf to match what we need. I have thought of creating a
new cdf from scratch, but more as a check on what Affy did than anything
else (as well as to redefine/delete their probesets that they created
for the controls and gridding probes). I did not actually know that
there was content missing from the cdf, so maybe this will give me
impetus or maybe someone else would like to do it! (there are writeCdf
functions as part of affxparser)
Best,
Elizabeth