Hi all, I would want to compare results from different article using different micrarray platforms: 1. I have experiments hybridized on the Affymetrix hgu133plus2 and i want to compare them against those from affymetrix hu6800 chip. In the Affymetrix website, I have not found the probes equivalent on the two platforms in the array comparison spreadsheets. I have the unigene cluster id and the genbank accession number for these probes ... How can I safely find the equivalent probes ? 2. I have the same problem to resolve but from the Affy hgu133plus2 chip and a specific cDNA platform. Again I have trhe unigene cluster id and the genbank accession number. Can you help me ? Thanks in advance :) -- Benjamin Haibe-Kains [http://www.ulb.ac.be/di/map/bhaibeka/] PhD student in the Machine Learning Group (MLG) [http://www.ulb.ac.be/di/mlg/] Universite Libre de Bruxelles (ULB) E-mail: bhaibeka@ulb.ac.be MicroArray Unity [http://www.bordet.be/servmed/array/index.htm] Institut Jules Bordet (IJB) E-mail: benjamin.haibekains@bordet.be

See http://www.camda.duke.edu/camda03/best_presentation/ I believe a more detailed MS is in preperation. Regards David N. Stivers, Assistant Professor Dept. of Biostatistics and Applied Mathematics, Bioinformatics Section University of Texas M. D. Anderson Cancer Center Houston, Texas

On Fri, Oct 15, 2004 at 06:06:39PM +0200, Benjamin Haibe-Kains wrote: > Hi all, > > I would want to compare results from different article using different > micrarray platforms: > > 1. I have experiments hybridized on the Affymetrix hgu133plus2 and i > want to compare them against those from affymetrix hu6800 chip. In the > Affymetrix website, I have not found the probes equivalent on the two > platforms in the array comparison spreadsheets. I have the unigene > cluster id and the genbank accession number for these probes ... How can > I safely find the equivalent probes ? matchprobes, has for some number of years now ,provided this functionality. > > 2. I have the same problem to resolve but from the Affy hgu133plus2 > chip and a specific cDNA platform. Again I have trhe unigene cluster id > and the genbank accession number. > there are many issues here, you can do some sequence matching. You might alow want to look at, since just matching probes is not always the best thing to do. title = {A cross-study comparison of gene expression studies for the molecular classification of lung cancer}, author = {Parmigiani, G. and Garrett-Mayer, E. and Anbazhagan, R. and Gabrielson, E.}, journal = {Clincal Cancer Research}, year = {2004}, volume = {10}, pages = {2922--2927} } title = {Combining multiple microarray studies and modeling interstudy variation}, author = {Choi, J. K. and Yu, U. and Kim, S. and Yoo, O. J.}, journal = {Bioinformatics}, year = {2003}, volume = {19, Suppl. 1}, pages = {i84--i90}, } > Can you help me ? > > Thanks in advance :) > > -- > Benjamin Haibe-Kains > [http://www.ulb.ac.be/di/map/bhaibeka/] > > > PhD student in the Machine Learning Group (MLG) > [http://www.ulb.ac.be/di/mlg/] > Universite Libre de Bruxelles (ULB) > E-mail: bhaibeka@ulb.ac.be > > MicroArray Unity > [http://www.bordet.be/servmed/array/index.htm] > Institut Jules Bordet (IJB) > E-mail: benjamin.haibekains@bordet.be > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+

----- Original Message ----- From: "Robert Gentleman" <rgentlem@jimmy.harvard.edu> To: "Benjamin Haibe-Kains" <bhaibeka@ulb.ac.be> Cc: "Bioconductor Mailing List" <bioconductor@stat.math.ethz.ch> Sent: Friday, October 15, 2004 3:52 PM Subject: Re: [BioC] equivalent probes between microarray platforms > On Fri, Oct 15, 2004 at 06:06:39PM +0200, Benjamin Haibe-Kains wrote: > > Hi all, > > > > I would want to compare results from different article using different > > micrarray platforms: > > > > 1. I have experiments hybridized on the Affymetrix hgu133plus2 and i > > want to compare them against those from affymetrix hu6800 chip. In the > > Affymetrix website, I have not found the probes equivalent on the two > > platforms in the array comparison spreadsheets. I have the unigene > > cluster id and the genbank accession number for these probes ... How can > > I safely find the equivalent probes ? > > > matchprobes, has for some number of years now ,provided this > functionality. > > > > > 2. I have the same problem to resolve but from the Affy hgu133plus2 > > chip and a specific cDNA platform. Again I have trhe unigene cluster id > > and the genbank accession number. > > > there are many issues here, you can do some sequence matching. You > might alow want to look at, since just matching probes is not always > the best thing to do. You might want to look at the mergemaid package for the latter problem. Sean