Why are my results different from the LEfSe implemented on the Huttenhower Galaxy?

  1. The original LEfSe implementation, which is available on the Huttenhower Galaxy (Galaxy), considers the entire set of taxa (all taxonomic ranks) when performing LEfSe. In comparison, the MicrobiomeAnalyst implementation only performs LEfSe at the user’s specified taxonomic level.

  2. The original LEfSe implementation uses original p-values when determining significant taxa. Meanwhile, the MicrobiomeAnalyst implementation provides users the option to use either original or FDR adjusted p-value cutoffs to determine significant features.

When all parameters were set identical, the results were the same in our benchmark evaluation