Figure 2.
Simulation studies for comparing ADAPT with nine other DAA methods. We simulate synthetic metagenomics sequencing count data under two contrasting conditions using the SparseDOSSA framework. The number of samples is the same between the two conditions. We generate 500 replicates for each simulation setting and report the mean of performance metrics. (a) False positive rates (type I errors) of all methods except for ANCOM under simulation settings with no DA taxa. The total number of taxa is 500. The total sample size is 50 or 100. The average library size is the same (balanced) for two conditions at 104 or different (unbalanced) between two conditions (104 for one condition and 105 for the other). (b) False discovery rates and power under simulation settings with different proportions of DA taxa. The sample size is 100. The total number of taxa is 500. The proportion of DA taxa is 5%, 10%, 20%, or 30%. The average library size is 2×104 for both conditions. The average absolute abundance fold change of DA taxa is 5. The directions of absolute abundance changes of DA taxa may be balanced or unbalanced.

Simulation studies for comparing ADAPT with nine other DAA methods. We simulate synthetic metagenomics sequencing count data under two contrasting conditions using the SparseDOSSA framework. The number of samples is the same between the two conditions. We generate 500 replicates for each simulation setting and report the mean of performance metrics. (a) False positive rates (type I errors) of all methods except for ANCOM under simulation settings with no DA taxa. The total number of taxa is 500. The total sample size is 50 or 100. The average library size is the same (balanced) for two conditions at 104 or different (unbalanced) between two conditions (104 for one condition and 105 for the other). (b) False discovery rates and power under simulation settings with different proportions of DA taxa. The sample size is 100. The total number of taxa is 500. The proportion of DA taxa is 5%, 10%, 20%, or 30%. The average library size is 2×104 for both conditions. The average absolute abundance fold change of DA taxa is 5. The directions of absolute abundance changes of DA taxa may be balanced or unbalanced.

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