Hi Ramzi, >From what I understand about your problem, your question is what is the difference between group A and B. The answer would be in the contrast A - wild type vs contrast B -wild type, if wild type is a common control for both and not in the direct contrast of A-B. If this is your situation, you may also want to see ?genas in limma. Best wishes, Swapna [[alternative HTML version deleted]]

Swapna, Thank you for your reply. Following your advice I have taken a look at ?genas in limma. Biologically I am not toaly sure this approach makes more sense in regards to this experiment, but it is something I will discuss with the PI. Either way I would like to familiarize myself with ?genas, and I have a couple of questions. The function seems to return correlation between the two data sets as a whole. Does it do so on a gene by gene basis, (ie is gene X correlated) rather than just the overall correlation? Would computing a correlation for each gene even make sense statistically? Right now I can only see overall correlation. Thank you, Ramzi ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] On Behalf Of Swapna Menon [swapna30@gmail.com] Sent: Sunday, June 26, 2011 4:41 AM To: bioconductor at r-project.org Subject: [BioC] Subject: Re: Comparing Two Affymetrix Arrays Question Hi Ramzi, >From what I understand about your problem, your question is what is the difference between group A and B. The answer would be in the contrast A - wild type vs contrast B -wild type, if wild type is a common control for both and not in the direct contrast of A-B. If this is your situation, you may also want to see ?genas in limma. Best wishes, Swapna [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor