Warning messages running 'lefse_run.py'

Downstream analysis and statistics LEfSe
1

Hi there,

I met some warning messages when running ‘lefse_run.py’,
Do you have any advice?

Thanks
Lu

Warning: namespace ‘ggcor’ is not available and has been replaced

by .GlobalEnv when processing object ‘p_mental_jxz’

Warning: namespace ‘ggplot2’ is not available and has been replaced

by .GlobalEnv when processing object ‘p_mental_jxz’

Warning: namespace ‘scales’ is not available and has been replaced

by .GlobalEnv when processing object ‘p_mental_jxz’

Warning: namespace ‘ggnewscale’ is not available and has been replaced

by .GlobalEnv when processing object ‘p_mental_jxz’

Number of significantly discriminative features: 0 ( 0 ) before internal wilcoxon

No features with significant differences between the two classes

Number of discriminative features with abs LDA score > 2.0 : 0

2

Hmm, this is a warning I haven’t encountered before. Can you let me know what version of LEfSe you’re running? Did you install LEfSe using PyPi or some other way?
Thanks,
Meg