[BioC] analyze HuEx array using HuGene .cdf file

Henrik Bengtsson hb at stat.berkeley.edu
Fri Dec 12 11:33:45 CET 2008


to second what already have been said and explained; you cannot reuse
that CDF for a different chip type.  The chip types doesn't even have
the same number of probes.

Note that:

Robinson, M. D. & Speed, T. P. A comparison of Affymetrix gene
expression arrays. BMC Bioinformatics, 2007, 8, 449. URL:

did this kind of comparison across these chip types.   Mark Robinson
used aroma.affymetrix for this.  I'm sure he reads this thread so I
can correct me if I'm wrong.  He and Elizabeth Purdom (I think)
created custom CDFs for this, cf.


Hope this helps


On Thu, Dec 11, 2008 at 6:02 AM, shirley zhang <shirley0818 at gmail.com> wrote:
> Dear List,
> I have a quick question. Since the HuGene probes are largely a subset
> of the HuEx probes, we would like to use that subset of probes for the
> HuEx array, then compare the results with that of using HuEx's own
> core probes which we already have. For this purpose,  can I use
> HuGen's .cdf file to analyze HuEx arrays? If not, how to
> generate/modify a .cdf file based on HuGen probes to analyze HuEx
> array data?
> Thanks,
> Shirley
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