I have 2 questions about dispersion in edgeR. 1) The model implies that as sequencing depth increases, the power for testing differential expression comes to an asymptote. This seems odd. 2) Usually when using a shrinkage estimator, values of the original estimates shrink monotonely towards the common estimate. So, if one plots the moderated values against one another for 2 values of the shrinkage parameter, the plot should be monotone increasing. The plot was too big to attach, but what I did was: d10=estimateTagwiseDisp(d,prior.n=10) d30=estimateTagwiseDisp(d,prior.n=30) plot(d10$tagwise.dispersion,d30$tagwise.dispersion) I have not included my particular set of data, as I am pretty sure we see this for any set. This plot seems to imply that 2 genes could have the same moderated dispersion values at prior.n=10 and very different values at prior.n=30. This is not due to my --Naomi Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111