Understanding the meaning of beta diversity in shotgun data

[Nicholas_Bokulich]

Hi @sooni ,

Interpretation of beta diversity/group significance plots is the same as for beta diversity of any other data type. This is a common question, so much so that it is in our FAQs (which you should check if you have not seen them already):

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This topic is listed in the FAQs, giving an explanation of how to interpret the 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…

I hope that clarifies. Good luck!