Additional file 7.
Supplementary Figure S9. Comparison between LEfSe and Metastats using the synthetic data described in Figure 5 and in the Materials and methods. LEfSe was applied as detailed in the paper; for Metastats we used the default settings (that is, α = 0.05 and Npermutations = 1,000) and, as for LEfSe and KW, we disabled the per-sample normalization as the features are independent. (a,b) Metastats has a higher false positive rate (average 5%) than LEfSe (average below 0.5%) and lower false negative rate. (c) When the subclass information is meaningful (see Figure 5 for the representation of the dataset), LEfSe performs substantially better than Metastats both in terms of false positive and false negatives. Overall, on these synthetic data, Metastats achieves very similar results compared to KW (Figure 5) and neither of them can make use of additional information regarding the within-class structure, thus achieving poor results compared to LEfSe when such kinds of information are available.
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Segata et al. Genome Biology 2011 12:R60 doi:10.1186/gb-2011-12-6-r60