I am trying to analyze my dataset with LEfSe in ubuntu terminal.
There are no errors when I formatting and running LEfSe analysis from my feature table.
However, after the analysis (specifically, after the ‘run_lefse.py’ step), LDA difference was compared among ‘subjects’, not ‘classes’.
When I tested using tutorial data (hmp_small_aerobiosis.txt), same situation still occurred.
I installed LEfSe by conda with following command:
$ conda install -c biobakery lefse
and running LEfSe with :
$ lefse-format_input.py hmp_small_aerobiosis.txt hmp_small_aerobiosis.in -c 1 -s 2 -u 3 -o 1000000
$ run_lefse.py hmp_small_aerobiosis.in hmp_small_aerobiosis.res
$ lefse-plot_res.py hmp_small_aerobiosis.res hmp_small_aerobiosis.png
Resulting plot: It seems like LEfSe comparing among ‘subject’, not ‘class’.
I have no idea how to solve this problem.