[BioC] RNA-seq analysis and two-way ANOVAs

[Elena Sorokin]

Hello,

What R packages for differential expression analysis of mRNA-seq data 
are currently set up to do statistical testing with two main effects 
(two-way ANOVA)?

I know that the latest versions of DESeq and edgeR can do this for 
genes; I know DEXSeq can do this for exons; I don't think that the 
latest versions of baySeq, DEGSeq or cuffdiff [the latter of which is 
not in R, obviously] can currently do this. Would anyone in-the-know 
care to update that? If there's a new software package that I missed, 
please let me know about that too.

Thanks!
Elena