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

[Christos Hatzis]

Thank you Maria.

Yes, I did explore the Affymetrix csv annotation file yesterday and came to
the same conclusion.  Having the alignment of the exemplar sequences is
helpful in some cases but not specific enough.  I will try the UCSC track
for probe set alignments.  Thanks for the link.

Best wishes,
-Christos 

-----Original Message-----
From: bioc-sig-sequencing-bounces at r-project.org
[mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf Of Stalteri,
Maria A
Sent: Thursday, March 03, 2011 8:17 AM
To: bioc-sig-sequencing at r-project.org
Subject: [Bioc-sig-seq] 3'-5' position of Affymetrix probe sets

Hi,

I'm afraid my previous reply was unhelpful, the Affymetrix alignments are
for the consensus/exemplar sequences, so would probably give the same
genomic coordinates for all the probe sets.

The UCSC genome browser has tracks for the genomic alignments of the HG-U133
Plus 2 probes. You can download the underlying data from

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/affyU133Plus2.txt.gz


or the  affyU133Plus2.sql      file.

Best wishes,
Maria
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