[BioC] Is there annotation package for Affymetrix Human Exon 1.0 ST Array on bioconductor?

[Jinyan Huang]

Hi Marc,
Thanks for your suggestion. It is clear for this.

On Fri, Feb 18, 2011 at 8:29 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> 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 at 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 at fgcz.ethz.ch>
>> To: "Jinyan Huang" <huangjy.tongji at gmail.com>, "bioconductor mailman" <
>> bioconductor at 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 at r-project.org [
>> bioconductor-bounces at r-project.org] on behalf of Jinyan Huang [
>> huangjy.tongji at 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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>
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