Additional file 9: Figure S8. of Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

A. Spike-in retrieval as a function of number of positive samples, by dataset size. Aggregated results across 150 iterations of multiplicative spike-ins of magnitude 5 with 50% cases, in datasets A1, A1s, and A1m. Each dot represents a spiked OTU. The Y-axis displays its p value quantile (0 is lowest p value, 1 is highest p value) within that DA run, and the X axis shows how many samples are positive (nonzero) for that OTU. Results from the three datasets are overlaid with different colors and faceted by statistical method. B. Spike-in retrieval as a function of number of positive samples, by case proportion. Aggregated results across 150 iterations of multiplicative spike-ins of magnitude 5 with 10, 25, or 50% cases, in dataset A1. Each dot represents a spiked OTU. The Y-axis displays its p value quantile (0 is lowest p value, 1 is highest p value) within that DA run, and the X axis shows how many samples are positive (nonzero) for that OTU. Results from the three case proportions are overlaid with different colors, and faceted by statistical method. C. Spike-in retrieval as a function of number of positive samples, by spike-in magnitude. Aggregated results across 150 iterations of multiplicative spike-ins of magnitudes 0.5, 2, 5, 10, and 20 with 50% cases, in dataset A1. Each dot represents a spiked OTU. The Y-axis displays its p value quantile (0 is lowest p value, 1 is highest p value) within that DA run, and the X axis shows how many samples are positive (nonzero) for that OTU. Results from the different spike-in magnitudes are overlaid with different colors, and faceted by statistical method. (ZIP 16398 kb)