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 >
My status1.design file is set up as:
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