[BioC] affymetrix annotation

Tim Yates TYates at picr.man.ac.uk
Tue Dec 21 15:40:25 CET 2010


Glad you like it!

There is the xmapbridge bioconductor package which (in partnership with the xmapbridge application downloadable from the xmap site) can be used to draw your own plots over the top of xmap.


----- Reply message -----
From: "arne.mueller at novartis.com" <arne.mueller at novartis.com>
Date: Tue, Dec 21, 2010 12:02
Subject: [BioC] affymetrix annotation
To: "Tim Yates" <TYates at picr.man.ac.uk>

Hi Tim,

Thanks for the link, this is a great tool - easy to see/test if probes are 
located in exons, cool! Is it possible to upload custom tracks (like in 
ucsc) or would I need to run xmap on my own web-server? 

  thanks a lot for this link,


"Tim Yates" <TYates at picr.man.ac.uk> 
12/20/2010 10:29 PM

<arne.mueller at novartis.com>, <bioconductor at stat.math.ethz.ch>

Re: [BioC] affymetrix annotation

We map to the Ensembl genome, so it's probably not what you are after, but 
we have the 430A arrays in xmap and you can search for probesets by 
entering their ids into the search box top right


How it's of some help...


----- Reply message -----
From: "arne.mueller at novartis.com" <arne.mueller at novartis.com>
Date: Mon, Dec 20, 2010 16:32
Subject: [BioC] affymetrix annotation
To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>


I was wondering where the mapping from affy probeset Ids to genes 
(EntrezGene) is coming from (package mouse4302.db). 
mouse4302.db::mouse4302_dbInfo lists all data sources (URLs) However, 
what's the "original" link between an affy probeset and an EnterzGene Id, 
is it Netaffx? My problem is that I've an "interesting" probeset that is 
annotated with an EntrezGene in Netaffx but the mouse4302SYMBOL map 
contains NA for this probeset Id.

I'd be happy if someone could point me to some documentation how this 
annotation/mapping is derived or let me know what I'm doing wrong ...?

   thanks a lot for your help,

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