Can I run LEfSe only with Wilcoxon ranksum but not with kruskal-wallis test?
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14 months ago
dpc ▴ 210

Hi, I have run Lefse with two group of microbiome samples (test and control) by setting Kruskal_wallis p-value to 1.00 and wilcoxon to 0.05. I have set 1.00 for kruskal-wallis so that it runs but passes all. Now, I am seeing that the bacteria with p-values > 0.05 are also being recorded in the LEfSe output. Why? I just want to run lefse with only wilcoxon with p-value 0.05.

Thanks, dpc

Lefse • 374 views
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