I am having a difficult time understanding what the output files from some of my beta diversity analyses mean (I am using QIIME2 version 2018.6). My metadata includes a categorical variable with two levels: “Yes” (which means the samples were exposed to a certain treatment) and “No” (which means the samples were not exposed to that treatment).
First, I followed the Moving Pictures Tutorial and ran the
qiime diversity core-metrics-phylogenetic command to generate the core-phylogeny statistics and the PCoA (with unweighted UniFrac values) file. I then ran the
qiime diversity beta-group-significance command to run the PERMANOVA (with unweighted UniFrac values).
Here is the PCoA figure:
And here are the PERMAOVA results:
My first question is: even though the PERMANOVA results shows significance (p < 0.05), why do the box and whisker plots not appear to reflect this?
I also visualized the PCoA, as mentioned above. Since the PERMANOVA was significant, I expected to see more distinct clusters of the “Yes” and “No” datapoints, but as you can see, there is no apparent clustering. Can you help me understand why these results seem to be contradictory? I know to rely on p-values instead of visual images when assessing significance, but I do not understand why these figures do not seem to support the PERMANOVA results.
Thank you for your help!