Hello. I am using "affy" to process HG_U95Av2 chip. I want to know how each spot (probe cell) is aligned on a chip. When I read in a data using (Data <- ReadAffy( )) and write out to a file, each spot is numbered from 1 to 409600. How can I determine probe cells and their corresponding probe pairs and probe sets from this file? Is there a list that corresponds to these spot numbers? I also would like to find out which probe is aligned on which probe cell. Thank you.

I think you are looking for xy2indices. HTH, 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 >>> s0uchi02 <s0uchi02@louisville.edu> 11/12/03 09:45AM >>> Hello. I am using "affy" to process HG_U95Av2 chip. I want to know how each spot (probe cell) is aligned on a chip. When I read in a data using (Data <- ReadAffy( )) and write out to a file, each spot is numbered from 1 to 409600. How can I determine probe cells and their corresponding probe pairs and probe sets from this file? Is there a list that corresponds to these spot numbers? I also would like to find out which probe is aligned on which probe cell. Thank you. _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

I've had problems using xy2indices function, but to get a list of all the x and y locations for the hg_u95av2 chip, you can go and download the cdf file from: http://www.affymetrix.com/support/technical/libraryfilesmain.affx (you may need to register for affymetrix's website, which is free) You can then open up the cdf file in notepad, and look for the individual probe names. This is the response I received from affymetrix developer's network: >I'm afraid the only way to find this info out is to either part the CDF file or use the SDK and write a program to get the info. For now, the CDF file is an ASCII text file so you >can open it and search for 100001_at. You will see a section that describes the list of >>cells that are part of that probe set. Use the PBase and TBase values to determine whether >a CEL is a PM (PBase != TBase) or MM (PBase = TBase). Its tedious, I had to write a java program to parse the file for me. But if you are just looking for individual probes, you should be able to view it in notepad. hope this is helpful, Richard Park -----Original Message----- From: James MacDonald [mailto:jmacdon@med.umich.edu] Sent: Wednesday, November 12, 2003 10:28 AM To: s0uchi02@louisville.edu; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Probe Cell I think you are looking for xy2indices. HTH, 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 >>> s0uchi02 <s0uchi02@louisville.edu> 11/12/03 09:45AM >>> Hello. I am using "affy" to process HG_U95Av2 chip. I want to know how each spot (probe cell) is aligned on a chip. When I read in a data using (Data <- ReadAffy( )) and write out to a file, each spot is numbered from 1 to 409600. How can I determine probe cells and their corresponding probe pairs and probe sets from this file? Is there a list that corresponds to these spot numbers? I also would like to find out which probe is aligned on which probe cell. Thank you. _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor