[BioC] analyze HuEx array using HuGene .cdf file

Laurent Gautier laurent at cbs.dtu.dk
Thu Dec 11 15:40:37 CET 2008

shirley zhang 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?

I'd say that you mostly likely can't.

The CDF definition contains information relative to the relative spatial 
location of the features (probes) on the chip, and unless the HuGene is 
a subset also in the spatial sense of it (that is  "like HuEx but with 
probes missing from their location on the array").

> If not, how to
> generate/modify a .cdf file based on HuGen probes to analyze HuEx
> array data?

HuGen(e{0,1}), HuEx, or else, you should have the corresponding .cdf 
distributed with the arrays (and you'll contact Affymetrix if this is 
not the case).


> Thanks,
> Shirley
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