CODEWITHSUNDEEP
rstatisticsp-valueveganmultivariate-testing
mucl
mucl

Reputation: 113

R vegan: adjusted p values for permanova (adonis2)

I am running an analysis of variances on a large distance matrix using adonis2 as described here: https://www.rdocumentation.org/packages/vegan/versions/2.4-2/topics/adonis

That method is frequently used in microbiome analysis to calculate beta diversity. That's also what I would like to do, i.e. to find out whether my community composition differs in response to an environmental variable (continuous) Permanova returns one p value and there is no "official" post hoc test yet. That's where my question comes in:

I've come across publications saying they adjusted their permanova result using FDR/BH method. I cannot wrap my head around this. I'm confident I understand how FDR correction is calculated, I just don't see how that would be done for PERMANOVA, or, even more, how I would code it.

Can anyone help me out here?

Upvotes: 0

Views: 3369

Answers (1)

StupidWolf
StupidWolf

Reputation: 46978

Would be clearer if you provide an example of so-called publication. You are right that for each variable, permanova returns 1 p-value. However, if the model includes many variables, you would have 1 p-value for each variable and you need to correct for FDR.

For example in this publication looking at variation in gut microbiome, they wrote:

To calculate the variation explained by each of our collected host factors, we performed an Adonis test implemented in QIIME. Each host factor was calculated according to its explanation rate, and P values were generated based on 1,000 permutations. All P values were then adjusted using the Benjamini–Hochberg method.

You can also see an example of this in Table S2, I attached a screenshot here:

enter image description here

Upvotes: 0

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