Hi Rob, On Aug 1, 2014 2:20 PM, "rob yang" wrote: > > Hello DESeq community, > > I wanted to ask how basemean and log2foldchange are calculated. > > 1) From mcol(mcol(dds_fit)), the basemean is denoted as "basemean over all rows". But I can't pin down what "all rows" this means. For a single transcript, my manual mean calculation of all counts across all replicates, all conditions do not equal to the DESeq reported basemean for a single transcript. > Yes that is kind of funny, I should change it to say "columns" or "samples". It is just as Steve described, the mean of normalized counts for all samples in the dds. > 2) log2foldchange seems to be changing with the contrasting variable. This is a little surprising since I'd expect log2foldchange to be a static number when comparing two conditions, and the contrasting variables only dictate testing for significance, ie., p-value. > I don't follow. Can you say more what you mean by changing with contrasting variable Mike > Thank you in advance. > > -Rob > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]