Extended Data Fig. 4. Evaluations of FDR (mdFDR) and power in identifying DA taxa in (a) multiple pairwise comparisons against a reference group, (b) multiple pairwise comparisons, and (c) pattern analysis.

Synthetic datasets were generated using the PLN model¹⁸ based on the mean and covariance estimated from the QMP dataset²³. The X-axis shows the sample size per group, and the Y-axis shows the FDR (mdFDR) or power. Each panel title designates the proportion of true DA taxa. The depicted metrics represent mean values ± standard errors (indicated by error bars) derived from 100 simulation runs for each setting. Within the context of multiple pairwise comparisons, ANCOM-BC2-when implemented with the SS filter-effectively controlled FDR (mdFDR) while maintaining power akin to its performance without the SS filter. In the pattern analysis, ANCOM-BC2-both with and without the SS filter-most often maintained the FDR under the nominal level while achieving adequate power, barring the scenario with 90% DA taxa. In this instance, ANCOM-BC2-both with and without the SS filter-experienced power loss due to inherent assumptions in bias correction.