Hello everyone,

I would like to know if you could help me about knowing if I can use DESeq2 for the following design:

I have only 1 animal that has 12 timepoints. The 6 first timepoints are "before infection". The 6 last timepoints are "after infection".

Is it possible and relevant for you if I use DESeq2 to compare the 6 samples before infection (group A) versus the 6 samples after infection (group B) even if I have only one animal ? If yes, do you recommend to had also the "timepoints" variable in the DESeq2 model ?

I hope my question is enough clear.

Thanks

Léo

You can just use a two group comparison. Your inference will not generalize to other animals obviously, because you are only comparing within one animal.