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

[Carlson, Marc R]

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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