[BioC] edgeR Quasi-likelihood with tagwise dispersion?

Ryan C. Thompson rct at thompsonclan.org
Tue Mar 19 01:44:59 CET 2013

Hi Gordon,

I was looking in the devel code for edgeR and I noticed this new check 
in glmQLFTest:

 > if(!is.null(disptype)) if(disptype=="tagwise") stop("glmfit should be 
computed using trended dispersions, not tagwise")

which refuses to run the quasi-likelihood F-test on a fit for tagwise 
dispersion. Could you elaborate on this? Does glmQLFTest implement its 
own different kind of tagwise behavior that is different from that of 

What would happen if I ran glmQLFTest after estimateGLMTagwiseDisp 
(using the release version, which does not disallow it)?Would the 
results be statistically meaningful? I have been doing this sometimes 
because I assumed that glmQLFTest was supposed to be a "drop-in" 
replacement for glmLRT, using all the same dispersions and such, due to 
this quote from the glmQLFTest help text in the current release of edgeR:

 > [glmQLFTest] behaves the same as ‘glmLRT’ except that it replaces 
likelihood ratio tests with quasi-likelihood F-tests for coefficients in 
the linear model.

So, what is the correct usage of glmQLFTest with the estimate*Disp 
family, and has this changed between the current release and devel 
versions of edgeR?


-Ryan Thompson

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