degrees of freedom - permanova

User Support
1

Hi,
Anyone knows how can i know the degrees of freedom from PERMANOVA?

Thanks

2

Two ways:

  1. Use qiime diversity adonis, which will report Df in the visualization
  2. For beta-group-significance you can calculate Df manually. I believe for this test Df = n - 1 where N = the number of unique groups (for categorical variables) or Df = 1 (for numeric variables) but you should check the original article to confirm.
1 Like
3

Hi, thank you for your reply.

The Df from adonis is the same from the permanova?

And, what do you mean with beta-diversity? I did permanova with bray curtis matrix.

1 Like
4

Beta diversity is the difference / distance between samples. So the distance matrix of distances between samples shows the beta diversity of those samples. :straight_ruler: :triangular_ruler:

(Alpha diversity is the richness and/or evenness of each individual sample, while beta diversity is between samples.)

Colin

1 Like
5

To add to @colinbrislawn’s point, your Bray-Curtis matrix is a beta-diversity matrix. Bray Curtis is one measure of beta-diversity.

6

Yes i know but, i did permanova with bray curtis matrix so, i got a little confused when @Nicholas_Bokulich gave me those two options.

So, what i want to know is how can i determine the Df from Permanova (that was done with bry curtis matrix)?

Thank you

7

I answered this question above. You say you did permanova with a bray curtis matrix, so if you did this in QIIME 2 you must have used one of the two methods that I described above. Even if you did not do this in QIIME 2, then my answer above still answers your question. Here's the answer:

8

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.