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 test and the log ratio and LDA score, but no p-value. Is there a way to make LEfSe provide the p-value from the kruskal wallis? Here’s the command I ran:
run_lefse.py formatted_cntrl_ace.in test_lefse_pval.res --wilc 0