Hi, I did DESeq2 for my data with simplified code: phyloseqtodeseq2(phyloseq.genus, ~ allGroups). The variable allGroups consists of eight groups in the experiment. Then I have the result table with all its amazing details, I draw boxplots for every genus which has statistically significant adj p-value. Every plot has eight groups (as eight boxplots) and one genus with its CLR abundance which differentiates between these groups. My question is, How can I know which of these eight groups has the highest amount of that genus and the second-highest and so forth.

Regards

Wisam

We don't have any automatic procedure for post-hoc tests after you find a difference across groups.

You can use contrast to make pair-wise comparisons. You can look into the stageR Bioconductor package for providing error control for post-hoc testing.