Depends on how you want to do it: 1) Can you combine all the samples and then do differential expression? I would argue no because even though the U133A probes are a subset of the U133plus2 probes (I recall reading this), the U133plus2 uses additional probes in each probesets to measure gene expression levels. So you would be getting different gene expression values for each gene depending on the microarray. 2) Can you do differential expression analysis on each microarray platform by itself, analyze it separately and combine the results? I think you would probably have more luck and less criticism doing this. Since they are both microarray platforms made by the same company, Affymetrix, you can have more confidence in combining the results. This is different from saying comparing the results from RNA-Seq to Microarray since you are dealing with two different platforms and protocols. Hope that helps! Fong

many ways to find common genes between U133A and U133plus2 if you can read chinese, i can send my working history to you i did the same work -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253