jwdebelius
October 7, 2022, 5:05pm
2
Hi @SingeunOh ,
Welcome to the :qiime2: forum!
I would recommend using the permdisp test (it's called betadispr in R). It's implemented in the beta-group-significance function; check the documentation to see which flag you need to use. The one caveat to this test is that it requires categorical data.
Best,
Here's some more discussion of the test, and idea:
An earlier post by @CarlyRae first introduced me to the fact that when examining beta diversity I need to consider not only the results of a multi or univariate anova, but also examining if the within-group distances to a centroid were equivalent among my groups. I'm wondering how to best interpret the situation where everything turns out to be significant. That is, if the results of both PERMANOVA and PERMDISP suggest significant differences, where do most people go next? I've run these tests b…
Hey all,
I have read quite a few other posts on this but I am not sure I understand the solutions fully.
To sum up my experiment, I have conditioned soil with different cover crop treatments for 3 months and I want to see if the fungal communities differ under those cover crop treatments. I understand the PERMANOVA results but is there a test to tell if the dispersion in one group is larger than another (if some treatments cluster tightly vs others being spread out on the PCoA)? You can visual…
For one of our paper, we need to calculate betadisper before PERMANOVA analysis. Is there a way to calculate betadisper statistics from qiime2 results in R or in qiime2 directly?
Thanks
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