Additional file 7: Figure S6. of Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

A. False positive rate distributions for datasets A1s–A3s and A1m–A3m. Violin plot of distributions of false positive rate (FPR) in 150 iterations for datasets A1s–A3s and A1m–A3m (vertical panels), analyzed with all differential relative abundance methods (horizontal panels). FPR is defined as the fraction of OTUs with p < 0.05. P values were not corrected for multiple testing. Black dots represent medians in each distribution. B. Area under the curve distributions for multiplicative spike-ins in datasets A1s–A3s and A1m–A3m. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each multiplicative spike-in magnitude in datasets A1s–A3s and A1m–A3m (vertical panels), analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. C. Area under the curve distributions for additive spike-ins in datasets A1s–A3s and A1m–A3m. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each additive spike-in magnitude in datasets A1s–A3s and A1m–A3m (vertical panels), analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. D. Area under the curve distributions for mixed multiplicative spike-ins in datasets A1s–A3s and A1m–A3m. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for mixed multiplicative spike-in magnitudes in datasets A1s–A3s and A1m–A3m (vertical panels), analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. (ZIP 4027 kb)