Pairwise Permanova

[Negin]

The pairwise Permanova test for comparing beta diversity gives me samples sizes that do not make sense. Is that the samples size of how many of each species do I have or it is referring to microbial sample size because I did not have the numbers of samples that QIIME is showing.

[Nicholas_Bokulich]

Hi @Negin,
Please see here for an explanation of those sample sizes:

Unifrac Significant Group over-inflating n's

Hey @saatkinson, Thanks! I was able to re-run your command to look at the results. For the figures, the n doesn’t represent the number of samples, but rather the number of pairwise comparisons that make up the distribution for the metric that the box-plot represents. For example, your 2920X_Control vs 2920X_Control has a sample-size of 7, and so the number of possible pairwise comparisons would be \frac{7 * (7-1)}{2} = 21 which matches what we see in the second figure. To state it a…