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

[Christos Hatzis]

Hi Maria,

Thanks again.  I could not find the link to the Ensembl Oligo probes file
that you suggested.
I'd appreciate that link if you have it.

But I was able to locate the BED file that feeds the UCSC custom track for
Affymetrix probe sets.  It can be downloaded from the NetAffx web site:

http://media.affymetrix.com/analysis/downloads/expression_array_bed_files/HG
-U133A.hg19.bed.gz

This file provides the chromosomal coordinates for the exemplars (track 1)
and for the individual probes in the probe set (track 2), in case others are
looking for this type of information.  Both are in the same file.

Best wishes,
-Christos

-----Original Message-----
From: Stalteri, Maria A [mailto:mastal at essex.ac.uk] 
Sent: Thursday, March 03, 2011 11:25 AM
To: christos.hatzis at nuverabio.com
Subject: RE: [Bioc-sig-seq] 3'-5' position of Affymetrix probe sets

AffyProbe became Oligo probes and it still exists, there is a link to it
from the 
Ensembl Microarray Probeset Mapping page.

Maria


________________________________________
From: Christos Hatzis [christos.hatzis at nuverabio.com]
Sent: Thursday, March 03, 2011 2:20 PM
To: Stalteri, Maria A; bioc-sig-sequencing at r-project.org
Subject: RE: [Bioc-sig-seq] 3'-5' position of Affymetrix probe sets

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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