Hi all, As we all know, rma & gcrma return log2 values, while li-wong and mas5 results are unlogged. I'm pretty sure that limma wants logged data, but how about multtest? Thanks in advance, Ken

Ken Termiso wrote: > Hi all, > > As we all know, rma & gcrma return log2 values, while li-wong and mas5 > results are unlogged. I'm pretty sure that limma wants logged data, but > how about multtest? Although multtest uses a permuted null distribution and thus there is not necessarily an assumption of normally distributed (or at least roughly symmetrical) data, I think it is still prudent to log. This is because you are still using means, which are not robust to outliers. > > Thanks in advance, > Ken > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.