It is also likely worth studying

http://www.bioconductor.org/packages/2.7/bioc/vignettes/oligo/inst/doc/V5ExonGene.pdf

which shows how NetAffx annotations can be collected and attached to exon
chip representations.  You can get a lot of mileage out of the
pd.huex.st.1.0.v2 with oligo package for analyzing exon arrays

On Fri, Feb 18, 2011 at 2:09 PM, Carlson, Marc R <mcarlson@fhcrc.org> wrote:

> Hi Jinyan,
>
> So there is not presently a package for this.  And is a little more
> complicated since this is an exon chip and the gene annotations are all
> gene-centric.  But you could still generate an annotation package if you had
> a mapping between the exon probesets and some kind of universal gene
> identifier (like an entrez gene ID).  If you have a mapping like this
> (probeset to gene) you could then easily generate a package by following the
> SQLForge instructions in AnnotationDbi here:
>
>
> http://www.bioconductor.org/help/bioc-views/release/bioc/html/AnnotationDbi.html
>
>
>  Marc
>
>
>
> ----- Original Message -----
> From: "Michal Okoniewski" <michal.okoniewski@fgcz.ethz.ch>
> To: "Jinyan Huang" <huangjy.tongji@gmail.com>, "bioconductor mailman" <
> bioconductor@r-project.org>
> Sent: Thursday, February 17, 2011 3:32:06 AM
> Subject: Re: [BioC] Is there annotation package for Affymetrix Human Exon
> 1.0 ST        Array on bioconductor?
>
> Chances are that there is no such thing :)
> Use exon.pmcdf from xmap.picr.man.ac.uk and exonmap/xmapcore.
> If you want gene level summaries - go for Brainarray CDFs.
>
> Cheers,
> Michal
> ________________________________________
> From: bioconductor-bounces@r-project.org [
> bioconductor-bounces@r-project.org] on behalf of Jinyan Huang [
> huangjy.tongji@gmail.com]
> Sent: Thursday, February 17, 2011 12:05 PM
> To: mailman, bioconductor
> Subject: [BioC] Is there annotation package for Affymetrix Human Exon 1.0
> ST    Array on bioconductor?
>
> Hi list,
>
> At this websites
> http://www.bioconductor.org/help/bioc-views/release/data/annotation/,
> I cannot find it.
>
> Thanks.
>
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