LEfSe feature names dependency

[sma]

Hi -
This seems to be related to this thread:

Problem with LEfSe

I hope you are doing well. I am reaching out with what I think is a serious problem with LEfSe. We have just realized that modifying names of features (e.g. genes or species) changes the results of the analysis. For example,in one dataset I am currently working on, replacing “sp._oral_taxon” with “HOT” to make the names shorter, results in 21 differentially abundant species instead of 22, and the LDA score also changes. When I tried to replace the species names with just numbers, I get 16 di…

Could you check if the discussion there clarifies the issue?
Thanks!
Siyuan