The bioBakery help forum

Interpreting LEfSe Galaxy output

Hi! I have a question about interpreting LEfSe output. When using the Galaxy platform to perform LEfSe, results say that 0 discriminate features with an abs LDA score > 2.0 are found. When I run the analysis with an abs LDA cutoff score of 1.0, I obtain 40 features above the cutoff. Then, when I graph those results with the LDA cutoff of 1.0, it appears that there are several taxa with LDA scores greater than 3.0 in the plot. How is it that the analysis reports 0 features with LDA scores > 2.0 yet features with higher LDA scores show up in the plot?

Thank you in advance! Your input is much appreciated!

Hmm I’m not sure why that might be happening. If you’d be willing to send over your feature table, I could try running it and troubleshooting, if you’d be comfortable–you can send it to be via direct message if you prefer.
Best,
Meg

Hi Meg,

Thank you for your help and for the offer to troubleshoot! However, no need, as I tried performing the analysis again and this issue did not replicate.

Best,
Fran