Uh…I just want to know that how to get the R^2 when calculating the p-values by PERMANOVA or Krushkal-Wallis test?
It confused me for several days. Thanks!
Great question. I’m not sure if the R-squared values are reported by the Qiime 2 plugins for these tests.
I’m pretty sure the adonis test can report R-squared values. Have you considered using that instead of PERMANOVA?
https://docs.qiime2.org/2019.1/plugins/available/diversity/adonis/
Colin
Thank you so much.
I reported R-squared values successfully!
However, in my opinion, this plugin (qiime diversity adonis) is called PERMANOVA.
It’s right?
This plugin is called diversity
This action is called adonis
vegan-R adonis is another implementation of the permanova test
permanova is also used in qiime diversity beta-group-significance
, so when @colinbrislawn says:
He most likely means try adonis
instead of beta-group-significance
(which does not report R2 values).
Thank so much! I got it.
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.