The bioBakery help forum

Data plotted for LEfSe visualization

Good morning,

I would like clarification as to what data is used to plot the LEfSe results on the galaxy pipeline. As I understand, the LDA result should output a tabulated file with the log of the highest mean among all classes, followed by the class with the highest mean and then the logarithmic LDA score.

But there are 4 columns of data in the tabulated output and I am not sure which column is used to plot the LEfSe results on the galaxy module.

My analysis aims to identify taxa which are discriminative for soil amendments(class). I’ve attached a portion of the LEfSe results I have for your reference and appreciate a clarification.

Thank you,
Daniel

LEfSe_help.csv (979 Bytes)

Hi,

The four columns for each feature, in order, are: log of the highest mean among all classes, (the following three only present if the feature is discriminative) class with the highest mean, the logarithmic LDA score, and KW p-values. The log LDA scores are plotted in visualization.

Thanks,
Siyuan

Thank you for the clarification @sma!

Best,
Daniel