Dear Prof Gordon, Thanks for your suggestion. Have a nice day. Best regards, KJ Lim On 25 January 2013 03:21, Gordon K Smyth <smyth@wehi.edu.au> wrote: > Dear KJ Lim, > > It may depend on the specific data, but I think that > > y <- estimateGLMCommonDisp(y,**design) > y <- estimateGLMTagwiseDisp(y,**design,trend=FALSE) > > is probably sufficient for SAGE data, whereas > > y <- estimateGLMCommonDisp(y,**design) > y <- estimateGLMTrendedDisp(y,**design) > y <- estimateGLMTagwiseDisp(y,**design,trend=TRUE) > > is advisable for RNA-seq data. > > Best wishes > Gordon > > > Date: Wed, 23 Jan 2013 14:01:35 +0200 >> From: KJ Lim <jinkeanlim@gmail.com> >> To: Bioconductor mailing list <bioconductor@r-project.org> >> Subject: [BioC] edgeR: estimateGLMTrendDisp or estimateGLMCommonDisp >> >> Dear edgeR community, >> >> Good day. >> >> Please forgive me if I ask a stupid question. >> >> May I ask, using trended dispersion to estimate genewise (tagwise) >> dispersion for multi factors experiment design is better than using common >> dispersion? >> >> Thanks for your time and advice. >> >> Best regards, >> KJ Lim >> >> > ______________________________**______________________________**____ ______ > The information in this email is confidential and inte...{{dropped:10}}