PERMANOVA Output

[ari_sh70 (Armin)]

Hello everyone!

I have 48 samples that divided to two groups ( MOL = 26 , PIC = 22 ). As I expected they are significant.
In the first plot (Distances to MOL) it is written that "MOL (n = 325) and PIC (n = 572)". What are these "n" here?

Best,
Armin

[Nicholas_Bokulich]

Hi @ari_sh70,

@ari_sh70

What are these “n” here?

The Ns in this plot are not number of samples, but rather number of pairwise comparisons. See an explanation here:

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…

@ari_sh70

I have 48 samples that divided to two groups ( MOL = 28 , PIC = 20 ).

Judging from your PCoA plot here, it looks like the sample sizes are MOL=26, PIC=22:

alpha and beta output problems

Now I have 48 samples, and the beta diversity graph is showing that there is a significance between two farms (blue and red dots) but on the other hand the p-values is saying that they are not significant. What could be the scientific reason behind that? Beta diversity graph [Screenshot%20from%202019-12-10%2007-22-17] P-value: [Screenshot%20from%202019-12-10%2007-23-19] Thank you all

[ari_sh70 (Armin)]

@Nicholas_Bokulich

See an explanation here:

ok thanks. I am going to read that

@Nicholas_Bokulich

Judging from your PCoA plot here, it looks like the sample sizes are MOL=26, PIC=22:

You are absolutely right. My mistaken. I apologize.