[BioC] analyze HuEx array using HuGene .cdf file

[shirley zhang]

Hi All,

Thanks for all of your help.

Since we already have 80 HuEx chips data, we want to
reanalyze these HuEx data by only looking at those probes on HuGen
array, then to see whether we get similar results as before. If the
result is consistent, we are happy to switch the platform in our other
studies.  In order to find the matched probes between HuEx and HuGene,
I looked at  the data that has already been generated at Affymetrix
that compares the probes from the Exon array with the Gene array at

http://www.affymetrix.com/support/technical/byproduct.affx?product=huexon-st.

This kind of data is exactly what I want. However, those comparison
files, for example "Human Exon 1.0 ST to Human Gene 1.0 ST, Best Match
(zip, 485 KB)" only includes the best matched probeset Ids between
HuEx and HuGene.  Where can I get the matched probe Id between  these
two platforms? If I can get the matched probe Ids, I can modify HuEx
CDF file in the way that masking those probes not found in Hugene
array as NA/missing, and then use this modified .cdf file to analyze
exon array.

Thanks again,
Xiaoling

On Fri, Dec 12, 2008 at 5:33 AM, Henrik Bengtsson <hb at stat.berkeley.edu> wrote:
> Hi,
>
> 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:
> http://www.biomedcentral.com/1471-2105/8/449/abstract/
>
> 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.
>
>  http://groups.google.com/group/aroma-affymetrix/web/huex-1-0-st-v2
>
> Hope this helps
>
> Henrik
>
>
>
> 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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>