Hi,
I have obtained slightly contrasting results regarding statistical differences in alpha diversity measurements among multiple treatments.
When I run the code for testing alpha diversity significance in Qiime2 (in a conda environment), I obtain the following output:
| Group 1 | Group 2 | H | p-value | q-value |
|---|---|---|---|---|
| 1 (n=75) | 2 (n=69) | 7.427362 | 6.42E-03 | 7.14E-03 |
| 3 (n=55) | 53.455151 | 2.65E-13 | 5.29E-13 | |
| 4 (n=60) | 84.749824 | 3.39E-20 | 1.69E-19 | |
| 5 (n=60) | 87.54449 | 8.24E-21 | 8.24E-20 | |
| 2 (n=69) | 3 (n=55) | 34.954631 | 3.37E-09 | 4.82E-09 |
| 4 (n=60) | 78.219153 | 9.22E-19 | 2.31E-18 | |
| 5 (n=60) | 81.851862 | 1.47E-19 | 4.89E-19 | |
| 3 (n=55) | 4 (n=60) | 30.352853 | 3.60E-08 | 4.50E-08 |
| 5 (n=60) | 40.739812 | 1.74E-10 | 2.90E-10 | |
| 4 (n=60) | 5 (n=60) | 3.550441 | 5.95E-02 | 5.95E-02 |
But when I export the Shannon's diversity metrics computed by Qiime2 with the core-metrics-phylogenetic command and apply Kruskal Wallis test statistics with FDR correction I obtain the following output:
| .y. | group1 | group2 | n1 | n2 | statistic | p | p.adj | p.adj.signif |
|---|---|---|---|---|---|---|---|---|
| shannon_entropy | 1 | 2 | 75 | 68 | 1.610244909 | 0.107344401 | 0.119271557 | ns |
| shannon_entropy | 1 | 3 | 75 | 50 | 5.828281837 | 5.60009E-09 | 1.12002E-08 | **** |
| shannon_entropy | 1 | 4 | 75 | 60 | 10.23648298 | 1.36094E-24 | 6.8047E-24 | **** |
| shannon_entropy | 1 | 5 | 75 | 60 | 11.24764854 | 2.37849E-29 | 2.37849E-28 | **** |
| shannon_entropy | 2 | 3 | 68 | 50 | 4.264521576 | 2.00331E-05 | 2.86187E-05 | **** |
| shannon_entropy | 2 | 4 | 68 | 60 | 8.487756672 | 2.10664E-17 | 5.2666E-17 | **** |
| shannon_entropy | 2 | 5 | 68 | 60 | 9.476555615 | 2.62815E-21 | 8.7605E-21 | **** |
| shannon_entropy | 3 | 4 | 50 | 60 | 3.702198552 | 0.000213739 | 0.000267174 | *** |
| shannon_entropy | 3 | 5 | 50 | 60 | 4.616832215 | 3.89642E-06 | 6.49403E-06 | **** |
| shannon_entropy | 4 | 5 | 60 | 60 | 0.959275879 | 0.337419784 | 0.337419784 | ns |
As you can see, the Qiime2 output is saying that all pair-wise comparisons are significantly different except for 4 VS 5, meanwhile the output from the rstatix package says that 1 VS 2 and 4 VS 5 are not significantly different. My question is, which one is the right one? Or perhaps I am considering the wrong threshold for q-value, namely 0.05?
Cheers,
Pablo
