Deseq2 paired analysis with correction for strength of intervention

Question

[amelia.tlm]

I have been trying to do a paired differential expression analysis using deseq2. This is an intervention study where I have "pre" and "post" measurements and would want to correct for the strength of intervention (ideally the intervention would be the same but I cant force people to go to the gym).

I have tried running a paired deseq analysis with intervention covariate set to zero for all pre samples and the strength of intervention for all "post" samples. The design for my deseq model is as such:

design=~ID+Strength of Intervention+Condition

I am not sure this is the right way to correct for this, would anyone be able to advise? Many Thanks!

Answer 1

[Devon Ryan]

Just get rid of Condition, you've already taken care of that in a non-binary form with Strength of Intervention.