Custom cdfs

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Jan 30, 2008, 3:31:20 PM1/30/08
to aroma.affymetrix
Hi, I am posting this question to the general group and will respond
momentarily. Best, Elizabeth

Hi Elizabeth,
I'm interested in a miRNA that is present on the HuEx array- PSR ID
3170700 (extended); but is not included in the Affymetrix CDF (2005
unsupported release). This PSR is documented in NetAffx and mapped to
the UCSC genome. Are the custom CDFs you created utilizing the data as
it is released in NetAffx and as such is more up-to-date than their
'unsupported' CDF file? Any suggestions?

Elizabeth Purdom

Jan 30, 2008, 3:55:34 PM1/30/08
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)

Elizabeth Purdom

Jan 30, 2008, 4:55:05 PM1/30/08
Another comment: my memory was that only 1 'main-design' probeset from
the NetAffx annotation did not show up on the cdf. But the miRNA are not
included in the main-design, I believe. I'm working off of memory right
now, so someone chime in if I'm wrong. Best, Elizabeth
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