The results of conda lefse and R run_lefse are different.

[LeeJH5120]

The results of conda lefse and R run_lefse are different.

What's the reason ??

in R run_lefse(norm_cpm.df, wilcoxon_cutoff = 0.05, group = "Type",taxa_rank = "Species", kw_cutoff = 0.05, multigrp_strat = TRUE, lda_cutoff = 2)

in conda (lefse) Change format to norm_cpm.df -> hmp_aerobiosis_small.txt lefse_format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3

lefse_run.py hmp_aerobiosis_small.in hmp_aerobiosis_small.res

lefse_plot_res.py hmp_aerobiosis_small.res hmp_aerobiosis_small.png

[KitHubb]

Hello, In my opinion, the difference in results may be caused by the number of bootstrap. Try raising it to 999 or higher.