Issues using LEfSe

Downstream analysis and statistics LEfSe
1

I am new to LEfSe and am trying to do a LEfSe analysis for a human milk microbiome dataset I have, and I seem to be having difficulty getting LEfSe to read in my file and format it for analysis. I
Once I hit “Execute” on the dialog box to Format Data for LEfSe, I get this error (Traceback (most recent call last):
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 435, in
feats = numerical_values(feats,params[‘norm_v’])
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 174, in numerical_values
feats[k] = [float(val) for val in v]
ValueError: could not convert string to float: MN2544_VT1303

I’d really appreciate some guidance!

Thank you,
Collin

[Here’s the input file I can’t seem to upload]
Organized otu_table_rows_final (1).tsv (20.4 KB)

2

Hello,
So sorry it took me this long to get back to you. The problem comes from having an extra row in your dataset–you have RandomID, which is likely your “subject” variable, and AGE, which is your “class” variable, but ID doesn’t have a designation in the dataset and therefore creates problems. If I delete the row with the ID variable, I’m able to get the data to load in properly.
Best,
Meg