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:[email protected]] Sent: Thursday, March 03, 2011 11:25 AM To: [email protected] 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 [[email protected]] Sent: Thursday, March 03, 2011 2:20 PM To: Stalteri, Maria A; [email protected] 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: [email protected] [mailto:[email protected]] On Behalf Of Stalteri, Maria A Sent: Thursday, March 03, 2011 8:17 AM To: [email protected] 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 _______________________________________________ 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
