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!