Table 2.
Differential abundant analysis methods evaluated in this study
| Method | Addressing compositional effects | Handling zeros | Model | Covariate/confounder adjustment |
|---|---|---|---|---|
| GMPR + Wilcox | GMPR | None | Wilcoxon rank-sum test | ✗ |
| TSS + Wilcox | Total sum scaling (TSS) | ✗ | ||
| Rarefy + Wilcox | Rarefaction (TSS equivalent) | ✗ | ||
| GMPR + DESeq2 | Geometric mean of pairwise ratios (GMPR) | Model (overdispersion) | Negative binomial model | ✓ |
| GMPR + edgeR | GMPR | Model (overdispersion) | Negative binomial model | ✓ |
| Wrench + MSeq | Wrench | Model (zero inflation) | Zero-inflated log-normal model | ✗ |
| RAIDA | Reference | Model (zero inflation) | Zero-inflated log-normal model | ✗ |
| ANCOM-BC | Bias correction | Pseudo-count | Log-linear model | ✓ |
| DACOMP | Reference | None | Wilcoxon rank-sum test | ✗ |
| LDM | TSS | None | Linear model | ✓ |
| Omnibus | GMPR | Model (zero inflation) | Zero-inflated negative binomial model | ✗ |
| Aldex2(Wilcox) | Centered log-ratio transformation (CLR) | Bayes | Wilcoxon rank-sum test | ✗ |
| Aldex2(glm) | Generalized linear model (GLM) | ✓ | ||
| GMPR + glm | GMPR | Model (overdispersion) | GLM (quasi-Poisson) | ✓ |
| Corncob | TSS | Model (overdispersion) | Beta-binomial model | ✓ |
| MaAsLin2 | TSS | Pseudo-count | Log-linear model | ✓ |
| eBay(Wilcox) | CLR | Empirical Bayes | Wilcoxon rank-sum test | ✗ |
| ZicoSeq | Reference | Empirical Bayes | Linear model | ✓ |