I have been using your excellent online LEfSe tool to perform LDA analyses in order to determine the OTUs that significantly discriminate biofilm compositions on different material surfaces. However, I have noticed that I get different results based on whether I feed in the OTUs as a unique code or enter them as a taxonomic hierarchy. e.g. ‘ASV_0000000238’ vs. ‘Bacteria| Proteobacteria| Alphaproteobacteria| Caulobacterales| Hyphomonadaceae’
I tend to get far more significantly discriminant results when I put them in as a unique OTU code and sometimes they don’t match up consistently with the results when the hierarchy is used.
I was wondering whether there is something about the tool that intrinsically accounts and adjusts for the taxonomic hierarchy in some way - and if you would be able to advise which method is more accurate? This sort of analysis is new to me - so I apologise if I am missing something obvious.