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.