Hi Binita, I have done comparisons of affy and codelink. I used limma on both. I used no background adjustment for codelink and quantile normalization. I then got a common gene list from TIGR's Resourcerer: http://www.tigr.org/tigr-scripts/magic/r1.pl Good luck, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html ********************************************************************** ********* Message: 17 Date: Thu, 28 Oct 2004 10:42:52 +0200 From: Binita Dutta <binita.dutta@vib.be> Subject: [BioC] Comparison of Affymetrix and CodeLink chip To: bioconductor@stat.math.ethz.ch Message-ID: <6.0.0.22.1.20041028104202.01ebd468@194.78.28.203> Content-Type: text/plain; charset="us-ascii"; format=flowed Dear All, I have been using limma for data analysis of affymetrix chips. We want to compare result of affymetrix chip and Amersham Codelink. We have done experiment with three knock out mice and compared with the wild type mice. Can you suggest us the best bioconductor packages which can be used to fish out differentially experessed genes with P. values on affymetrix and codelink slides. Help in this regard will be highly appreciated. Binita ============================== Binita Dutta, PhD MicroArray Facility(MAF) UZ Gasthuisberg Onderwijs en Navorsing Herestraat 49 3000 Leuven Belgium