I'm trying to run a differential expression analysis of RNA-seq data with limma but I'm not sure how to proceed and was hoping to get some suggestions from you.
I have 18 samples from two similar experiments (9 and 9). Each experiment has three treatment groups of which two are the same across the two experiments, and only the control group changed. What I'd like to do is to analyze everything together considering Experiment as a Batch effect and therefore ending up with 4 total treatment groups (two with 6 replicate samples each and two with 3 samples each). Could you suggest how to do this, if it makes sense at all?