I have data from a randomized clinical study evaluating a treatment effect (Treat vs. Placebo). Samples were collected at baseline and end of treatment (Time: Baseline vs. Final). I want to to identify bacterial taxa changes from associated with Treat, and each subject served as their own control over time and exposure . I was wondering if I could use the following lines?

Any suggestion would be greatly appreciated!

design(dds) <- ~ SubjectID+Time + Treat + Time:Treat dds <- DESeq(dds, test="LRT", reduced = ~ SubjectID+Time + Treat)

Yes this design will pull out the differences over time, controlling for the difference at base line, while also each subject has their own placebo baseline.