HiAll, I want to know from Affymetrix for HGU_95Av2 chip (all the probes) where on the human genome the probes will align to?! Basically what regions on the chromosomes the probes were designed for? For example 1000_at probeset has 16 probes and i want to know where on the human genome each of these probes align to, i want start and stop positions for each of the probes alignment? Thanks in advance. Hrishi

Pardon my ignorance. How would i get the chromosomal locations written to a text file for all the probes on HGU_95Av2. Thanks, Hrishi --- James MacDonald <jmacdon@med.umich.edu> wrote: > hgu95av2CHRLOC in the hgu95av2 package. > > Best, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > >>> Hrishikesh Deshmukh <d_hrishikesh@yahoo.com> > 05/21/05 3:03 PM >>> > HiAll, > I want to know from Affymetrix for HGU_95Av2 chip > (all > the probes) where on the human genome the probes > will > align to?! > Basically what regions on the chromosomes the probes > were designed for? > For example 1000_at probeset has 16 probes and i > want > to know where on the human genome each of these > probes > align to, i want start and stop positions for each > of > the probes alignment? > > Thanks in advance. > Hrishi > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > ********************************************************** > Electronic Mail is not secure, may not be read every > day, and should not be used for urgent or sensitive > issues. >

Thank you very much sir, just one more question. The annotation file gives the "region" for each probeset_Id but is it possible to get the start and stop cooridnates for each of the 16 probes of a probeset_id. For ex. ProbeSet_ID| x|y| probeIndex| StartChrLoc| StopCHRLOC 1000_at 1 2 1 42545499 42545524 . .. ... 1001_at......................... I wonder where can i find this information. Thankyou very much again. Hrishi --- "James W. MacDonald" <jmacdon@med.umich.edu> wrote: > Hrishikesh Deshmukh wrote: > > Pardon my ignorance. > > How would i get the chromosomal locations written > to a > > text file for all the probes on HGU_95Av2. > > If all you want is the chromosomal locations in a > text file, I would > simply download the annotation file from Affy, and > delete all the other > columns. > > http://www.affymetrix.com/Auth/analysis/downloads/taf/HG_U95Av2_annot_ csv.zip > > This information is in the Genome Alignment column > of the file. > > Best, > > Jim > > > > > -- > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 >