They wouldn't be exactly consistent even if they used the same prior count, since the calculations are not identical. edgeR normalizes the prior count by each library's normalization factor so that log fold changes are always squeezed toward zero, while voom, if I understand correctly, does not normalize the prior count so that all log counts will be on the same scale, at the cost of accepting some small bias in the squeezing.
On Wed, Feb 15, 2017 at 11:01 PM Dario Strbenac <dstr7...@uni.sydney.edu.au> wrote: > Good day, > > The cpm function in edgeR uses a default offset of 0.25 and voom in limma > uses 0.5 (and provides no user modification) to calculate the base 2 > logarithm of the counts per million. Might these be made consistent? > > -------------------------------------- > Dario Strbenac > University of Sydney > Camperdown NSW 2050 > Australia > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
