Lefse command skipping all iters because too few groups or not enough contrast


Experiment overview:
I have 12 subjects. Each of my subjects had a treated and an untreated sample taken (A and B) over 5 time points (0, 3, 7, 14, 30). I also have an additional control group from a skin scraping for 2 of my subjects ( C ).

I am trying to run a lefse command on my data and all the iters error out in this way:

[WARNING]: Skipping iter 1 in LDA test. This can be caused by too few groups per class or not enough contrast within the classes.

I am using the command: mothur >
lefse(shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.1.subsample.1.pick.shared, design=status1.design)

My status1.design file is set up as:
Sample. Group
1_A_0. A0
1_A_3 A3
1_B_0 B0
1_B_3 B3

I am wondering if one of the options for the lefse command might help with this?? I checked the command on the MothurSOP but was unsure which option might best help.

Many thanks. JM

It sounds to me like lefse is not the command you want. You likely want a paired comparison (treated and untreated from same person) and repeated measures (same person over time). Lefse won’t do that. I’d suggest talking to a statistician about the proper test for this design.


This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.