Hi Christian,

Thank you for your reply. I have created scheme file for exon arrays. But I
am still not sure how to get the annotation for the genes which are
extracted from the analysis througth the package. Generally when I used
bioconductor, I use "annotate" or cdf package to get the gene information,
but for exon array what should I do? as you mentioned it has no official
annoation package for this type array, I guess I may not use "annotate"?
Probably I have to directly load transcript csv and extract information from
it manunally?
Do you have idea about it? What I want is gene symbol and location (start,
end). If your package has function to directly extract such info as
"annotate" does, it would be great. Do you have any idea? Thanks.



On Thu, Sep 10, 2009 at 4:36 PM, cstrato <cstrato@aon.at> wrote:

> Dear ZRL?
>
> You can have a look at:
> http://www.bioconductor.org/docs/workflows/oligoarrays/
>
> For example, package xps allows you to do RMA for exon arrays and do
> summarization on the probeset level or on the transcript (gene) level.
>
> P.S.: There is no official version of "HuEx-1_0-st-v2.cdf" only an
> unsupported version since for exon arrays Affymetrix uses the
> "HuEx-1_0-st-v2.r2.pgf" file.
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
> V.i.e.n.n.a           A.u.s.t.r.i.a
> e.m.a.i.l:        cstrato at aon.at
> _._._._._._._._._._._._._._._._._._
>
>
> zrl wrote:
>
>> Dear list,
>>
>> I am current starting to analyze some human affy exon arrays
>> (HuEx-1_0-st-v2). I have several questions as below:
>>
>> 1. when I did the analysis, I can not find a offical version of CDF file,
>> "HuEx-1_0-st-v2.cdf", Could anyone point me to the location where I can
>> download this file?
>>
>> 2. after I read the CEL files and did RMA normalization for all the
>> features/probes, how can I map the probe sets back to the genes? The
>> results
>> I want are the genes with the gene name/symbol, location on genome, and
>> expression values for the gene.
>>
>> 3. what is the best software for such analysis?
>>
>> Thank you very much.
>>
>> -ZRL
>>
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>>
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>>
>
>

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