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: [email protected] [mailto:[email protected]] On Behalf Of Mike Smith Sent: Friday, March 04, 2011 8:57 AM To: Stalteri, Maria A Cc: [email protected] 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
