Hello,

I was wondering if anyone could take a look at how I'm conducting my Differential Gene Experiment and confirm whether it is correct or not.

To describe my experiment:

I have patients at a baseline, a "before" time point, and an "after" treatment time point. I want to compare them pairwise to check the effect of treatment on gene expressions and compare each sample against its baseline. I took the advice from this discussion (DESEq2 Paired samples Before and after treatment ) and designed my comparison as:

design ~ patient + treatment and I ran DESeq2 with full comparison (Wald test) [ddsMat <- DESeq(ddsMat)]

I was wondering if this is indeed the correct way to do pair-wise comparisons or if I would need to make any other changes to the script to carry this out.

Thank you so much for the advice/insight!

Paired designs are covered in the vignette FAQs, please use the code suggestions from there to be in line with recommended best practices.

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#can-i-use-deseq2-to-analyze-paired-samples