Table 2.
Results in analysis of the two real datasets
| Testing the global hypothesis |
Testing individual OTUs |
||||||||
|---|---|---|---|---|---|---|---|---|---|
| Trait | MiRKAT | P-FL | VE-freq | VE-arcsin | VE-omni | VE-freq | VE-arcsin | VE-omni | DESeq2 |
| URT microbiome data | |||||||||
| Smoking | 0.0019 | 0.0018 | 0.0070 | 0.0006 | 0.001 | 4 | 14 | 5 | 0 |
| PPI microbiome data | |||||||||
| gPC1 | 0.22 | 0.19 | 0.13 | 0.47 | 0.19 | 0 | 0 | 0 | 14 |
| gPC2 | 0.36 | 0.19 | 0.19 | 0.19 | 0.26 | 0 | 0 | 0 | 49 |
| gPC3 | 0.24 | 0.31 | 0.30 | 0.21 | 0.29 | 0 | 0 | 0 | 29 |
| gPC4 | 0.16 | 0.088 | 0.013 | 0.080 | 0.021 | 0 | 1 | 0 | 13 |
| gPC5 | 0.0094 | 0.015 | 0.034 | 0.010 | 0.015 | 0 | 3 | 3 | 48 |
| gPC6 | 0.19 | 0.41 | 0.43 | 0.49 | 0.53 | 0 | 1 | 1 | 23 |
| gPC7 | 0.15 | 0.21 | 0.76 | 0.16 | 0.22 | 0 | 0 | 0 | 59 |
| gPC8 | 0.21 | 0.33 | 0.64 | 0.36 | 0.47 | 1 | 0 | 0 | 4 |
| gPC9 | 0.15 | 0.12 | 0.10 | 0.12 | 0.15 | 0 | 0 | 0 | 20 |
Note: P-FL, PERMANOVA-FL. For the global hypotheses, reported results are P-values. For the individual OTU tests, results reported are the number of OTUs detected at FDR = 10%. MiRKAT and PERMANOVA-FL results are based on the Bray–Curtis distance. In analysis of the URT microbiome data, MiRKAT and PERMANOVA-FL yielded P-values 0.005 and 0.0042, respectively, when the weighted-Unifrac distance was used, and 0.00078 and 0.0006 when the Hellinger distance was used.