[Bioc-sig-seq] 3'-5' position of Affymetrix probe sets

[Christos Hatzis]

Thanks, Mike.
This database is very helpful, and the flat file provides the data to
perform the analysis that I needed.

For others interested the NAR reference for this database is found below:

http://nar.oxfordjournals.org/content/38/suppl_1/D726.full.pdf+html

-Christos

-----Original Message-----
From: bioc-sig-sequencing-bounces at r-project.org
[mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf Of Mike Smith
Sent: Friday, March 04, 2011 8:57 AM
To: Stalteri, Maria A
Cc: bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] 3'-5' position of Affymetrix probe sets

Hi,


> The PLANdbAffy database provides flat files of probe annotation, assigned
> by a reannotation pipeline that the authors designed.  You can access it
> here:


http://affymetrix2.bioinf.fbb.msu.ru

<http://affymetrix2.bioinf.fbb.msu.ru/>I've not looked at the flat file for
U133 Plus 2 itself, but just entering the three probeset IDs you listed into
their web form you can see the probes that make up the three probesets all
map to different places.  The three links below go to USCS with a track for
each probeset shown.

206527_at - http://bit.ly/g8XcZK
209459_s_at - http://bit.ly/g5bPn8
209460_at - http://bit.ly/eU2mpG

I imagine it would be fairly straightforward to download their flat file,
break it up by probeset ID and then find the maximum and minimum coordinates
of the constituent probes.

-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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