[BioC] analyze HuEx array using HuGene .cdf file

[shirley zhang]

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,
Xiaoling




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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
>