Hi, I had a related question regarding BCV, it has been my recent experience that working in vivo with heterogeneous tissues such as brain yields a much higher BCV than 10%, usually close to 30% even though I am working with genetically identical organisms (mice, all males as well). Is that your observation as well, or does this mean that variation is being introduced at some of the sample processing steps? I do not have technical replicates, although I have n=5 biological replicates for each of my conditions Interestingly, filtering out low count reads does not seem to lower the average BCV much thanks very much for your answer Lucia On Fri, Aug 10, 2012 at 9:40 PM, Gordon K Smyth wrote: > See fourth paragraph of the Discussion of the edgeR glm paper: > > http://nar.oxfordjournals.org/**content/40/10/4288.long > > Gordon > > Date: Fri, 10 Aug 2012 11:45:31 +0300 >> From: KJ Lim >> To: Bioconductor mailing list >> Subject: [BioC] edgeR: Value of variation of biological variation (BCV) >> >> Dear edgeR users and R community, >> >> I'm analysing a set of RNA-Seq data which has 2 different genotypes >> (treeHS, treeLS) and time of treatment (0H, 3H, 24H, 96H) with edgeR. >> >> After carried out estimating the common dispersion, the value of BCV >> for my RNA-Seq data was 0.428. >> > hl <- estimateGLMCommonDisp(hl, hl.design, verbose=TRUE) >> Disp = 0.18319 , BCV = 0.428 >> >> May I ask, it is common to see the value of variation of biological >> variation (BCV) as such? What this value can tells about the RNA-Seq >> data? I have these thoughts wondering me for a while. Forgive me if I >> have asked a stupid question. >> >> Thank you very much for your time. >> >> Have a nice weekend. >> >> Best regards, >> KJ Lim >> >> > ______________________________**______________________________**__________ > The information in this email is confidential and inte...{{dropped:13}}