[BioC] CDF/CEL files

Laurent Gautier laurent at cbs.dtu.dk
Tue Apr 22 04:28:44 MEST 2003

On Mon, Apr 21, 2003 at 02:07:07PM -0600, Ann Hess wrote:
> I am trying to use the information in CDF files from the BioConductor
> website (www.bioconductor.org/data/cdfenvs/cdfenvs.html).
> Although there are 287296 (536x536) probes on an hu6800 chip, I only get
> 281966 probes (from 7129 "genes") in the hu6800cdf data.  I counted the
> probes for each "gene" and added to get a total of 281966.
> Am I missing duplicates?  What am I doing wrong?  My objective is to merge
> the CEL and CDF files so that I can perform my own analysis.
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Not all the probes on a chip correspond to genes. Some are controls for
(for gridding), some others are more mysterious to me....

I won't ask too many questions about your objectives, but I would trend
to think that 'affy' and 'makecdfenv' would take care of the job for you.

Hopin' it helps,


currently at the National Yang-Ming University in Taipei, Taiwan
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent

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