Hi, I am a PhD student the University of Lisbon and I am performing several analysis of differential expression (using edgeR). Reading edgeR manual I am not sure about the dispersion value that I should use. I am comparing libraries of the same species (non model species) subjected to different experimental conditions. In the manual you say that "Typical values for the common BCV (square- root-dispersion) for datasets arising from well-controlled experiments are 0.4 for human data, 0.1 for data on genetically identical model organisms or 0.01 for technical replicates." The species that I am studying is not Homo sapiens and despite it is the same species (and then genetically identical), individuals to be compared are not clones of each other. Can you please help me so I can decide which dispersion value to use. Thank you for your attention, Tiago Jesus -- output of sessionInfo(): none -- Sent via the guest posting facility at bioconductor.org.

Hi Tiago, Just a quick comment ? when the manual is talking about "Typical values for the common BCV ?", that is in the context of analyses with no replicates. You do not mention whether you have replicates, but if you do, then it is generally better to use them to estimate the dispersion. If you do not have replicates, then you have to use your judgement. In addition, take the P-values with a grain of salt (as it says in the manual, "Note that the p-values obtained and the number of signi cant genes will be very sensitive to the dispersion value chosen"). Best, Mark On 01.07.2013, at 12:53, Tiago Jesus [guest] <guest at="" bioconductor.org=""> wrote: > > Hi, > > I am a PhD student the University of Lisbon and I am performing several analysis of differential expression (using edgeR). Reading edgeR manual I am not sure about the dispersion value that I should use. I am comparing libraries of the same species (non model species) subjected to different experimental conditions. > > In the manual you say that "Typical values for the common BCV (square-root-dispersion) for datasets arising from well-controlled experiments are 0.4 for human data, 0.1 for data on genetically identical model organisms or 0.01 for technical replicates." > > The species that I am studying is not Homo sapiens and despite it is the same species (and then genetically identical), individuals to be compared are not clones of each other. Can you please help me so I can decide which dispersion value to use. > > Thank you for your attention, > > Tiago Jesus > > -- output of sessionInfo(): > > none > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 ---------- Prof. Dr. Mark Robinson Bioinformatics, Institute of Molecular Life Sciences University of Zurich http://tiny.cc/mrobin