[BioC] edgeR questions

[Wang, Li]

Dear List Members

My experimental design is set to contain two groups of RNA-seq and within each group there are two subgroups(each subgroup with 8 replicates). Our goal is to identify differential expression genes between two groups and also between two subgroups. 
I red through the case studies in edgeR user guide and has not found such cases.  
How can we achieve the goals with edgeR?
My current idea is to do the analysis between subgroups first and then between groups. In the case, we can find the shared and different DE genes. 
I donot know if we can do the analysis in one run. 
Any comments and suggestions are very much appreciated. 
Thanks in advance!

Best wishes
Li