Hi all, For a bit more background (and for the sake of posterity), Gordon has previously discussed the rationale of tunable (or not) prior.counts in edgeR::cpm and voom in this support forum thread:
https://support.bioconductor.org/p/59846/#59917 -steve On Thu, Feb 16, 2017 at 8:00 PM, Dario Strbenac <dstr7...@uni.sydney.edu.au> wrote: > Good day, > > Now I notice the differences in how the prior counts are applied. In edgeR's > cpm: > > prior.count.scaled <- lib.size/mean(lib.size) * prior.count > lib.size <- lib.size + 2 * prior.count.scaled > ... ... > t(x) + prior.count.scaled > > but in limma's voom: > > t(counts + 0.5)/(lib.size + 1) > > Basically, the values added to the counts and the library size ignore the > library size of each sample in the voom function. > > -------------------------------------- > Dario Strbenac > University of Sydney > Camperdown NSW 2050 > Australia > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Steve Lianoglou Bioinformatics Scientist Cancer Immunology Genentech _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
