Question about LEfSe input_format.py when specifing no subclass

[sma]

Hi,
Many apologies for the long time to reply! If you didn’t find a solution, here’s a work-around to output p-values, while “not running” Wilcox filtering:

P-values not calculated when wilc = 0

Hello, I have a dataset that is comparing multiple groups of samples and I previously had problems that the Wilcoxon test was being run even when I didn’t have subgroups. This forum helped me realize I needed to be using the --wilc 0 option to force it to not run the Wilcoxon test. My new problem arises in that now the p-values for the features passing the initial Kruskal-Wallis test are not being assigned a p-value. The output file is giving me a certain number of taxa that are passing the te…

Thanks!
Siyuan