I have two microarray datasets with sample information like below:

**Patient Replicates** -------- **Disease/Control** -------- **Muscle Type**


Patient A  ------------  Disease  ------------ X

Patient A  ------------ Disease  ------------ Y

Patient B  ------------  Disease  ------------ X

Patient B  ------------ Disease  ------------ Y

Patient C  ------------  Disease  ------------ X

Patient C  ------------ Disease  ------------ Y

Patient D  ------------  Control  ------------ X

Patient D  ------------ Control  ------------ Y

Patient E  ------------  Control  ------------ X

Patient E  ------------ Control  ------------ Y

I want to perform differential gene expression analysis to get the significantly expressed genes in Control vs Disease for both Muscle types. No need to compare between muscles.

How can I code this in R with limma/edgeR packages?