I want to compare pathway abundances generated using HUMAnN2, by LEfSe.
I merged tables across samples, and performed humann2_split_table, and now I have a raw table, a stratified table, and an unstratified table.
From my understanding, I should input a raw table to LEfSe, as in the MetaPhlAn2 tutorial they input a table which preserves the rank (not summarizing to a certain rank). However, I saw some websites and papers that input an unstratified table.
What input is desirable to perform differential analysis? Is it depending on the purpose of analysis?