The bioBakery help forum

LDA Effect Size errors

F_LefSe_RS_11_GenusTest1.txt (15.1 KB)

I was not able to process this data set at step[B) LDA Effect Size (LEfSe). Could you please try running it and see what might be the problem? Many thanks,


error message:
Number of significantly discriminative features: 70 ( 70 ) before internal wilcoxon
/galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/ RRuntimeWarning: Error in (function (file = “”, n = NULL, text = NULL, prompt = “?”, keep.

Hello Celine,
There are some characters in the taxon names in your data, such as quotation marks and brackets, that create problems for LEfSe. Once I removed those characters, I was able to get LEfSe to run successfully.
I hope that helps!