Hi, I have a bunch of cel files, part of them are in U133A, others are in U133plus2. Is there a way to RMA normalize them all together by only focusing on the common probe sets? or the RMA must be one in samples from each platform and think about a way to combine them? Thanks, -James [[alternative HTML version deleted]]

Hi James, Were these chips run separately (e.g., at different times)? If so, you are much better off normalizing each group separately and then combining. At about the same time that Affy started selling the U133-plus2 chip, they also started selling their own IVT kit, so it is possible that the 133A chips were run using the Enzo IVT kit, and the 133-Plus2 chips were run using the Affy IVT kit. If this is true then you most certainly would not want to combine until after running RMA. And maybe not even then. In our experience, the batch effect tends to overwhelm any possible biological differences when trying to compare Affy and Enzo processed data. Best, Jim On 8/14/2011 12:02 PM, James Anderson wrote: > Hi, > > I have a bunch of cel files, part of them are in U133A, others are in > U133plus2. Is there a way to RMA normalize them all together by only > focusing on the common probe sets? or the RMA must be one in samples > from each platform and think about a way to combine them? > > Thanks, > > -James > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues