I am in the process of performing analysis of microbiota data from a study where we compare three different groups (lets call them A, B, and controls). I have managed to perform the LEfSe analysis and form Cladograms for all three groups together, and observed some differences. However, while the overall bacterial communities that describe the individual groups are interestingly, the comparisons I am mostly interested in are comparing:
A vs control
B vs control
A vs B
I know from PCoA plots and other investigations that A and B are highly similar, but different from the controls. Thus I wish to perform the individual comparisons separately. My question is thus:
Can I perform the pairwise comparisons directly using LEfSe, or should I generate different input data.
Do you have any suggestions for correcting for multiple comparisons? E.g. BH?
I am currently working with the Galaxy module, and are starting to familiarize myself with the python package.
Thanks for the help