permanova and adonis results significance

[Alan_Chan (Alan)]

Hi all,

I am confused on the results of running qiime diversity beta-group-significance and qiime diversity adonis. When I run the former looking at a factor, let’s say site, I get a significant association with PERMANOVA. Then when I run the adonis test with site as well as other factors, it shows site as some R2 value but that it is not significant. How can a factor be significantly associated with a difference between groups but non significantly explain some portion of variation? Am I using these tests wrong? Is site in fact not significant then?

[Nicholas_Bokulich]

@Alan_Chan

Then when I run the adonis test with site as well as other factors, it shows site as some R2 value but that it is not significant

It is normal for significance to change when taking other effects into account. The R2 value is not an indicator of significance, though — when you say not significant, I assume you mean the P value no longer indicates significance.

You should check out these other topics for more insight:

Adonis vs. Anosim vs. Permanova

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