Hi, I’m new to LEfSe. After trying to get my data to work with LEfSe in Galaxy for a week now, I’ve got some results but also had a couple of unclear issues that I wish to be clarified here.
I generated LEfSe input file from QIIME2 16S feature table, collapsed it to level 7 and calculated relative frequency. I input this file in the Galaxy:
feature-table.csv (103.1 KB)
I wanted to compare between 2 classes, response (R) or non-response (NR) to treatment. There was no subclass.The process went smoothly and I got the nice looking LEfSe plot as shown here:
However, I am unclear with these two issues.
- There some groups of taxon in the same lineage showing up. For example:
When I check the LEfSE result table, each member in the same group has exactly the same LDA score. Is it normal to get the result like this? I’m not sure but I guess it’s because each of them is a singleton and there’s no other member in these taxa so they all showed up with the same LDA score. However, to have all of them in the plot make the information a bit redundant.
- There is k__Bacteria taxon enriched in R group with high LDA score. That’s weird because all features in both classes suppose to be bacteria. Is it because there’s also an Archaea feature in the data? If so, why don’t LEfSE calculate the other around (e.g. Archaea enriched in NR group)?