Hello, Dear
I would like to ask whether the first factor in DESeq2 should be set as the control or the treatment when the goal is to evaluate the changes in the treatment compared to the control.
Hi @09303030076
It entirely up to you/depends on your needs. If you swap the factors, upregulated genes will be marked as downregulated (another condition will be used as control). If you have a control condition, you probably want the genes up o downregulated against the control. Just try both options, check reads counts and how up and downregulated genes look like in the output data.
Hope that helps.
Kind regards,
Igor