I'm hoping to make a comparison between three sample groups, let's call them A, B and C. I want to know whether (A is more similar to C) or (B is more similar to C). I think can get a sense of that by doing PCoA. For example, in the PCoA emperor plot below, I can see that the orange group is generally closer to blue group and the red group is generally farther from the blue group, which suggests the composition of the orange group is more similar to the blue group (right?). What I'm wondering is if there is a more quantitative way of assessing this.
Similarly, I can tell from a permanova (attached) that the both the "sorted native rRNA" group and "barcoded rRNA" group are significantly different from the "unsorted native rRNA" group. But I can't tell if "sorted native rRNA" or "barcoded rRNA" is significantly larger/smaller.
Another way to put it is, per the diagram below, I'm trying to tell if distance A is significantly different from distance B
As best as I understand, the post-hoc test is telling me that barcoded is all the groups are statistically distinct from each other, and are forming distinct clusters, more-or-less. What I want to know is, is the Barcoded group more similar (i.e. closer in PCoA space) to the Unsorted Native group, or is the Sorted Native group more similar to the Unsorted Native group. Or are they both equally different from the Unsorted Native group
If this information is available from the permanova test, and I'm just misinterpreting it, that would be fantastic news, and I would love to hear it.
