Hello,

We are analyzing an RNA-seq experiment that was performed in cases and controls across two time points. We are interested in finding differentially expressed genes (DESeq2) and exons (DEXseq) between cases and controls that have the same effect at both time points. How do we best set this up in deseq/dexseq. We have 3 replicates of each set:

• 3 replicates cases/ 3 replicates controls - timepoint 1
• 3 replicates cases/ 3 replicates controls - timepoint 2

We want to analyze these all together to increase power. Should we add all 6 cases and 6 controls and add timepoint as a covariate in the model?

Thank you

See the DESeq 2 vignette. It has a FAQ when to split up experiments or not. See contrasts section for obtaining specific comparisons.