Hi, I am working on 16s rRNA data with two groups, one control and one treated measured over 8 timepoints. We collected a sample from both groups before giving any treatment to just check if the two groups were similar at start. Unfortunately when I look at deseq2 results for this timepoint, I see some taxa being differentially expressed with reasonable differences in their mean abundances.

Is there a way to correct for this difference ?

Thanks! Hena

As I've said previously on the support site, I'm not convinced DESeq2 is appropriate for microbiome or metagenomics data.

That said, you are describing an example from the workflow (time course, last example). Take a look how the design is set up.