Dear Galina, Getting a small dispersion is good, not bad. Your experiment is giving a bioligical CV of about 14% = sqrt(0.01859). In our experience, that is typical or even on the high side for controlled experiments. See comments in the discussion of the following paper: http://nar.oxfordjournals.org/content/early/2012/02/06/nar.gks042 Note that, while a dispersion 0f 0.019 may look small, it is still vastly different from assuming Poisson variability. You give a quote from the first case study of the edgeR User's Guide. That data was from an observational study on human tumours, obviously highly variable data. Best wishes Gordon ------------ original message -------------- [BioC] question about edgeR and Poisson model: common dispersion is too low Glazko, Galina V GVGlazko at uams.edu Tue Apr 10 16:26:03 CEST 2012 Dear list, dear Dr. Smyth I am analyzing RNA-Seq data for the first time and I am confused with the value of common dispersion. I have only two replicates between conditions (A1,A2: normal; B1,B2: oxidative stress) and the value of common dispersion is > d2<-estimateCommonDisp(d2) > d2$common.dispersion [1] 0.01859112 As far as I understand it is too low, is it? In the User Guide it is written that 'a common dispersion estimate of 0.2 means that there is a lot more variability in the data that can be accounted for by the Poisson model' My estimate is much lower. Does it mean that I have to use Poisson model instead of NB? If I have to use Poisson model, is it possible to do with edgeR package? I would appreciate your advices! Best regards Galina > sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_2.6.0 limma_3.12.0 BiocInstaller_1.4.3 loaded via a namespace (and not attached): [1] tools_2.15.0 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}