I also have a question about use of random effects with fitZig. I am currently trying to run the following model:
design = model.matrix(~0+var1+var2+var3)
dup <- duplicateCorrelation(MRcounts(MRexp),block=subject, design= design)
model = fitZig(obj = MRexp, mod = design, control = settings, useCSSoffset=FALSE, useMixedModel=dup$consensus)
This is what I understand to be correct from limma's user manual. However, when I then call res$dupcor, I get "NULL" -- as if that part of the model wasn't called.
In addition, the results of the above model are exactly the same when I don't call "useMixedModel".
My conclusion is that fitZig isn't incorporating the "useMixedModel" statement. Is this correct, or is something wrong with my model statement?
I am using metagenomeSeq version 1.12.0.
Thank you in advance for any help you can provide!