Hi all! Newbie here. I wondered wh ether quantile normalization should be done on an array containing all conditions of 1 experiment (eg containing both patients and healthy people) or within replicates of each condition (eg on data from patients and on data from healthy people separately)? Thanks indeed.

You should normalize all conditions together, unless you have reason to suspect that the assumptions for a quantile normalization (most genes are not differentially expressed) does not hold. Best, Jim On 5/30/2012 5:38 AM, Cytochalasin wrote: > Hi all! > > Newbie here. > > I wondered wh ether quantile normalization should be done on an array > containing all conditions of 1 experiment (eg containing both patients > and healthy people) or within replicates of each condition (eg on data > from patients and on data from healthy people separately)? > > Thanks indeed. > > _______________________________________________ > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099