How to report more than 3 digits after decimal for ADONIS p value

User Support
1

Hi,

I have revising some of my ADONIS figures and got a request from my PI to add more than 3 digits for p value. And this is because the variable on the spot got a p value as "0.050" which is on the edge. While I get the idea that it should make sense to be plotted as p > 0.05, not significant, however, is there a way to let QIIME2 produce p value in 4 or 5 digits after the decimal and I can simply re-run the code to get the real p value?

Best,
Shuqi

2

Hello @Shuqi.

Here are the docs for the adonis test. It's part of the R package 'vegan'

a list of control values for the permutations as returned by the function how , or the number of permutations required...

So the p-value shows 3 digits because, 999 tests are performed by default, and that leads to only 3 significant digits.

4 sig digs would require >1000 tests, 5 would require >10,000 tests.

In practice, I would run this with --permutations 9999 or --permutations 99999 if I wanted more resolution / stability in the p-value.
This takes 10x or 100x longer to run, so I would try the n_jobs flag to speed things up!

5 Likes
3

Thank you so much for your thorough explanation!

1 Like