Hello Ryan, Thanks very much for the clarification. It really helps. Regards On Thu, Jan 9, 2014 at 12:40 PM, Ryan C. Thompson wrote: > 1) Is it fine to use both common and trended dispersion? >> > > You can estimate both common and trended dispersions on the same DGEList > object, but only one of them will be used. The other will be ignored. I > believe that trended dispersion will always be preferred over common > dispersion if both are available. > > > 2) is there any specific conditions to use common or trended dispersion >> estimation? >> > > Well, broadly speaking, if you believe that there is a dependency between > mean and dispersion in your data, then you need trended dispersion. If not, > you would use common dispersion. A number of publications have argued that > when modeling RNA-seq data with the negative binomial distribution, such a > dependency exists. For example, the (I think) original DESeq paper: > http://genomebiology.com/2010/11/10/R106/ > > So generally you would always want to use trended dispersion if you are > analyzing RNA-seq. For other types of data, you would likely want to test > that assumption. > > -Ryan > -- Reema Singh Postdoctoral Research Assistant College of Life Sciences University of Dundee, Dundee DD1 4HN, Scotland United Kingdom http://www.compbio.dundee.ac.uk/people.html [[alternative HTML version deleted]]