I am performing a differential expression analysis with DESeq2, with these data:
- control, 2 replicates
- treatment, 2 replicates
So far there is still one obscure part of the manual for me: the design variable that you can set in many commands. I grasped the concept behind it but I am still struggling to understand how to use it properly. At the moment, I am using:
design = ~ condition
How would you set it, and why? Could someone write a couple of lines on how should I use that variable properly?
Any help appreciated!