Hi everyone I am trying to prepare my data for network analysis using MENA (http://ieg2.ou.edu/MENA). I am using the aggregate function in R to collapse the ASVs into their assigned taxonomy and I get 52 ASVs. Phyloseq is telling me I have over 100 in some of my treatments when I do my alpha diversity analysis. This is for archaea by the way
I'm not sure why this is?
I hope my question makes sense.