[BioC] edgeR Quasi-likelihood with tagwise dispersion?
Ryan C. Thompson
rct at thompsonclan.org
Tue Mar 19 01:44:59 CET 2013
I was looking in the devel code for edgeR and I noticed this new check
> 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?
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