LEfSe feature names dependency

[sagunmaharjann]

What I actually noticed is that the results of LEfSe seem to depend on
the feature names. Is this known? When I rerun several times the *.res
file had the same md5 checksum. When I change the names of e.g. OTUs
(from e.g. OTU_1, OTU_2, OTU_100, to OTU_001, OTU_002, OTU_100) but
leave the input file otherwise identical the LDA scores can be quite
different (up to 15%), yet reruns are again identical. Does some
sorting take place in the format_input.py?

[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