Dear Community,

My RNA-Seq experiment has three factors: A, B and C. A and B are random effects while C is fixed effect. I would like to fit a mixed model including all of the main effects and interaction terms, i.e.,

model=A + B + C + A x B + A x C + B x C + A x B x C

Can DESeq2 or edgeR fit the mixed model? Thanks.

When I searched "DESeq/DESeq2/edgeR random effect", I found this post: http://seqanswers.com/forums/archive/index.php/t-16539.html

Simon mentioned that uses shrinkage for random effect, and DESeq2 has already considered the shrinkage for dispersion and coefficient.

My Question is: how to use shrinkage in DESeq2 modeling so that I can fit the mixed model mentioned above.

Thanks.

Yanzhu

Unfortunately, I really need the random effects for my analysis, since I will use the variations explain by the random effects to do some calculation.

You should explain this in more details.

Why can't you use an F test to see whether the effect explains enough variation?