Dear All: 

I am using edgeR for RNA-Seq data analysis. According to the paper "Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation" by McCarthy, DJ et al. (2012), the tagwise dispersion model is recommended. It is a compromise between entirely individual genewise dispersion and the common dispersion models. 

My question is, is it possible to obtain a "pure genewise" model, i.e. there is NO shrinkage applied towards the common/trended dispersion? I think what I mean is to estimate \phi by maximizing APL_g (\phi) + G_0 * APL_s (\phi) where G_0 is set to zero (no shared part). Which argument in the estimateGLMTagwiseDisp function shall I change? Can I set prior.df = 0 to get a purely genewise model without any shrinkage? In the paper, G_0 = 20/df, but I am not sure if this "df" in the denominator is the prior.df argument in R, or something else.

Thank you very much!

Best,
Gu

Sent with Sparrow (http://www.sparrowmailapp.com/?sig)


	[[alternative HTML version deleted]]

