I have a question concerning the alpha diversity boxplots, on the qzv file that I attached, we can see that for the variable "n.family" the kruskal wallis statistical test is significant for all groups with a p-value of 0.02 but when I look at the kruskal wallis test in pairwise, I see that all the q-values (p-value corrected with Benjamini & Hochberg correction) are not below the threshold of 0.05. My question is what to do? Should I take into account the significance of this variable, or only take the uncorrected p-value? And if so, how would you present it in a publication? Thank you in advance
Hello!
This situation is quiet common. I think all, that you can report, is that alpha diversity was affected by this factor, but pairwise comparisons revealed no differences between groups.
You have a big number of groups and with p = 0.0298 (0.03) there is a great probability that all p-values in the pairwise test will be corrected to a higher values than 0.05. In addition, the number of samples within each of the groups is very low.
I would try to pool some of the groups (if it possible) to get smaller number of groups with higher number of samples. Or, if measures are repeated, try mixed effects.