[BioC] analyze HuEx array using HuGene .cdf file

shirley zhang shirley0818 at gmail.com
Thu Dec 11 23:01:45 CET 2008

Hi Larurent,

Thanks for your quick reply.  You are right, CDF file also includes
the location of probes on the chip. In that case, can I modify the
HuEx .cdf file to mask those probes not found in Hugene array as
NA/missing, and then use this modified .cdf file to analyze exon
array? If can, do you know how to do it in R or other tools?

Thanks a lot,

On Thu, Dec 11, 2008 at 10:40 PM, Laurent Gautier <laurent at cbs.dtu.dk> wrote:
> 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).
> L.
>> Thanks,
>> Shirley
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