I realized LEfSe provides different results from identical data sets in which only feature names have been modified. Compare the outputs below: the number of significant feature differ by 1 and the LDA scores changed for some features:
Anyone faced the same issue?
Hi - yes I have also had this issue, but just assumed that I had made a copy-paste error. Have you sorted it out?
Laura
Hi, I have also faced this problem. Have you found why that happened?
Hi @hlsw2001 @Laura_mason @DrNezar
The answer is cross-posted here: the way microorganisms are named affect the final results of lefse
In short, Lefse is picky about identifier formats. Clean those up and these technical problems will likely resolve.
