Dear BioC users, I was wondering wether it would not make sense to perform rma normalization on the 2 (or more) conditions we want to compare separately instead of alltogether as usually performed. This questioning comes from the three conditions I currently have to deal with. They clearly display different raw levels and I'm afraid that using global RMA will somehow hide an effect that could be meaningful. To illustrate I put in attachement the boxplots obtained before and after the two "types" of rma normalization. Did anyone already have to deal with such a problem? Do you have any suggestions? Many thanks for your help, Cl?mentine -- Cl?mentine Dressaire Post-doctoral research fellow Control of gene expression lab ITQB - Instituto de Tecnologia Qu?mica e Biol?gica Apartado 127, Av. da Rep?blica 2780-157 Oeiras Portugal +351 214469562

> dear Cl?mentine > i think? you should do globle RMA, if they are from the same platform, e.g. affymetrix U133 series > ?for different platform, like one is affy, the other is illumina i have no ideas > > -- 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

Dear Cl?mentine the short answer is 'no'. A slightly longer answer is that alternatives to RMA exist that are less aggressive in removing differences between arrays. There is a trade- off between removing unwanted technical variation and wanted biological variability. Different methods address the trade-off differently. Careful QA/QC on your data is needed, and you need to make sure that your experiment has the appropriate controls. In order to explore these issues (and in order to know how to defend your non-standard choice e.g. to reviewers), it would probably be best to contact a local statistician. Best wishes Wolfgang Btw, as always, the attachment (boxplot) did not make it through the mailing list. On 12/9/11 7:50 PM, Cl?mentine Dressaire wrote: > Dear BioC users, > > I was wondering wether it would not make sense to perform rma > normalization on the 2 (or more) conditions we want to compare > separately instead of alltogether as usually performed. > This questioning comes from the three conditions I currently have to > deal with. They clearly display different raw levels and I'm afraid that > using global RMA will somehow hide an effect that could be meaningful. > To illustrate I put in attachement the boxplots obtained before and > after the two "types" of rma normalization. > > Did anyone already have to deal with such a problem? Do you have any > suggestions? > > Many thanks for your help, > > Cl?mentine > > > > _______________________________________________ > 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 -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber