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waldronlab / lefser

R implementation of the LEfSe method
https://waldronlab.io/lefser/
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Conversion to relative abundance prior to lefser analysis #21

Closed agatadziegiel closed 10 months ago

agatadziegiel commented 1 year ago

Hi,

I am relatively new to using the tool but the implementation of LEfSe in R is very helpful! I have done some reading on LEfSe and it seems that many users (and the LEfSe paper) indicate that counts should be converted to relative abundances before analysis. I was wondering whether this is done automatically with lefser or if the user needs to do this first? I have tried looking at the example dataset and it seems that raw counts are used but I am not sure.

Thanks in advance!

coralzhang commented 1 year ago

I wonder if you have an answer to this yet? Should I normalize the data manually first?

lwaldron commented 1 year ago

Sincere apologies that we missed your question earlier... I'm working to identify a new maintainer for the package, and looking into the answer to this question.

lwaldron commented 10 months ago

To belatedly answer your question, yes, the data must be normalized manually first. Please accept our apologies for the delay and lack of documentation here.