Doubt about statistical test

[rparadiso (Rubina)]

Good morning to all,
I have a doubt about the statistical test to apply of my samples.
I have samples collected from three different sites of the same animal (rumen, intestine and feces).
I have two groups of animals (control and treated).
I’d like to know if in my case it is better to calculate alpha and beta diversity with longitudinal plugin (and use Mann Withney or Wilcoxon test ?) or alpha-group significance plugin that uses the kruskal wallis test?

thank you

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[jwdebelius (Justine Debelius)]

Hi @rparadiso,

It depends on the hypothesis you want to test. So, if you want to know if the individual rumens respond to the change in treatment, you would want to filter your alpha diversity or distance matrix and apply a kruskal wallis, adonis or permanova (most are implemented in q2-diversity; you can get a multivariate test for alpha diversity from anova in q2–longitudinal).

If you want to know about how the rumen/lumen/intestine differ in the same animal between the two treatments, then I would recommend the LMEs in q2-longitudinal.

When I’m doing a similar analysis, I will often mix the two techniques because they let me address different aspects of the same data.

Best,
Justine