[BioC] affy exon array analysis questions

cstrato cstrato at aon.at
Mon Sep 14 23:43:37 CEST 2009

Dear ZRL

Since I have never used the "annotate" package I am afraid that I cannot 
answer this question.

Package "xps" uses the official Affymetrix PGF, CLF, probeset.annotation 
and transcript.annotation files, and thus is able to provide gene symbol 
and location.

If you want to know how to use xps with exon arrays, there are two files 
located in subdirectory xps/examples, namely "script4xps.R" and 
"script4exon.R". Both scripts contain code examples which you mostly 
need to only copy/paste.

Best regards

zrl wrote:
> 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 at aon.at 
> <mailto:cstrato at 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 <http://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
>                [[alternative HTML version deleted]]
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