Hi,

I'm using DESeq2 to perform differential analysis on RNA-Seq data for three different timepoints (Baseline, Acute, Severe).

I've looked at differential genes for pairwise comparisons between timepoints: Acute vs. Baseline,  Severe vs. Acute, and Severe vs. Baseline.  

How would I make a design to test if genes from Severe vs. Baseline are different from Acute vs. Baseline ?

Thank you in advance!
 

See this related question:

A: [DESeq2] Difference between results from using contrast option and using name op