LEfSe comparing more than two classes

Hi everyone,

This is a question for the LEfSe galaxy module: I have a question about comparing more than two classes. Is this possible in the module? I tried this but the results were a bit unexpected.

When I compare, for example, class A and class B or A and C or A and B, I get several distinct differences. However, when I compare A, B, and C together, I get only one difference that never appeared in the individual comparisons? Is that an expected result? Would you have any advice on this? Thank you!

Hi @microbiome

There are a few versions of Lefse in the Galaxy community. I think Lefse only produces a single comparison per run for the versions hosted at ORG, EU, and AU. Not sure about Biobakery’s version. Maybe that explains your observations?