Dear community,

I have an RNA-seq project with three factors: A, B and C, where A and B are random effects, while C is fixed effect. As I know, DESeq2 and edgeR cannot take care of the random effect.

Is there any R package taking care of random effect for RNA-seq read counts gene expression data?

Thanks.

Yanzhu

No, there is no such package.

Such a package would be very hard to create, both computationally and theoretically. It would require the creation of new statistical theory (like limma, edgeR or DESeq2 but more so) and there isn't a lot of demand for such a thing.

The closest is the MAANOVA package, but that is for microarray data.