beta-group significance results.

[Nisha]

Hi,

I'm comparing healthy control samples with the diseased condition. I couldn't see any difference between the two groups using PCoA. But after running PERMANOVA, I got significant p and q values of 0.001.
How to interpret these contrasting results?

best
Nisha

[Mehrbod_Estaki]

Hi @Nisha ,
A similar question was asked and answered here, have a look there and let us know if you have any unanswered, additional questions. I'll also add that you should look into the key assumptions of the PERMANOVA test makes, one aspect of this can be checked using the PERMDISP test which is available within the diversity beta-group-significance.
Good luck!