On Feb 20, 2013, at 9:22 AM, Mark Robinson <mark.robinson at="" imls.uzh.ch=""> wrote: > > Davide, I recommend: > > cpm(y, normalized.lib.size=TRUE) > > y$pseudo.counts would or should be quite similar to the CPMs, but the latter is easier to explain. > Thanks Mark. Anyway, is it ok to use pseudo counts (if I'm able to explain)? Another thing, can I contact you privately when I'll try to implement calcNormFactors and estimateCommonDisp (and equalizeLibSize) in another language? Best, d > Best, Mark > > > > On 20.02.2013, at 07:22, Davide Cittaro wrote: > >> Hello list, >> I'm trying to use read counts normalized with edgeR outside R. After a DGEList has been normalized by TMM and dispersion has been estimate (at least with estimateCommonDisp) I have at least three ways to export data: >> cpm(y) >> cpm(y, normalized.lib.size=T) >> y$pseudo.counts >> >> Which would be the most appropriate? Actually I'm having really good results with pseudo.counts, but I would like to know your opinion about. >> >> Thanks >> >> d >> _______________________________________________ >> 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