[BioC] affy exon array analysis questions

[cstrato]

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
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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
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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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