Table 2.

Comparison of observed and expected consistency in differentially abundant genera across five diarrhea datasets.

Tool	No. sig. genera	Max overlap	Mean exp.	Mean obs.	Fold diff.	p
ALDEx2	57	3	1.141	1.544	1.353	<0.001
limma voom (TMM)	76	4	1.22	1.618	1.326	<0.001
MaAsLin2 (rare)	74	3	1.204	1.595	1.325	<0.001
ANCOM-II	15	3	1.033	1.333	1.29	<0.001
MaAsLin2	79	3	1.215	1.557	1.281	<0.001
Wilcoxon (rare)	88	4	1.269	1.625	1.281	<0.001
metagenomeSeq	66	3	1.164	1.485	1.276	<0.001
Wilcoxon (CLR)	82	3	1.22	1.549	1.27	<0.001
limma voom (TMMwsp)	85	4	1.239	1.565	1.263	<0.001
t-test (rare)	62	3	1.145	1.403	1.225	<0.001
corncob	87	5	1.275	1.552	1.217	<0.001
DESeq2	82	4	1.246	1.512	1.213	<0.001
LEfSe	119	5	1.408	1.613	1.146	<0.001
edgeR	138	5	1.509	1.667	1.105	0.002

No. sig. genera: Number of genera significant in at least one dataset; Max overlap: Maximum number of datasets where a genus was called significant by this tool; Mean exp.: Mean number of datasets that each genus is expected to be significant in (of the genera that are significant at least once); Mean obs.: Mean number of datasets that each genus was observed to be significant in (of the genera that are significant at least once); Fold diff.: Fold difference of mean observed over mean expected number of times significant genera are found across multiple datasets; p: p-value based on one-tailed permutation test that used the ‘Mean obs.’ as the test statistic. Note that <0.001 is indicated instead of exact values, because 0.001 was the minimum non-zero p-value we could estimate based on our permutation approach. Source data are provided as a Source Data file.