B) LDA Effect Size(LEfSe) error ! please help me!

Downstream analysis and statistics LEfSe
1

Hello,
I want to compare and analyze two groups.
So, lefse analysis was conducted using the Galaxy Web.

LEfse format file was created, but the .res file cannot be executed with an error as shown below.

My data is two groups, and the number of samples for each group is 1 and 7.
(# of samples FC group is 1, # of samples of OM group are 7.)

Is the error due to the difference in the number of samples in the two groups? Or is there an error with only one sample in a group?

Please help me and tell me a solution…!
I look forward to your response. Thank you!

lefse_input_C1qa-HFD-F-FC-vs-C1qa-HFD-F-OM.txt (70.7 KB)

/galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Error in svd(X, nu = 0L) : infinite or missing values in 'x'

  warnings.warn(x, RRuntimeWarning)
Traceback (most recent call last):
  File "/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/run_lefse.py", line 89, in <module>
    if params['rank_tec'] == 'lda': lda_res,lda_res_th = test_lda_r(cls,feats,class_sl,params['n_boots'],params['f_boots'],params['lda_abs_th'],0.0000000001,params['nlogs'])
  File "/export/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/lefse.py", line 189, in test_lda_r
    z = robjects.r('z <- suppressWarnings(lda(as.formula('+f+'),data=sub_d,tol='+str(tol_min)+'))')
  File "/galaxy_venv/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 359, in __call__
    res = self.eval(p)
  File "/galaxy_venv/local/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 178, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/galaxy_venv/local/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 106, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in svd(X, nu = 0L) : infinite or missing values in 'x'
2

Hi there,

I tried the file you attached and received the same error that you pasted on your post. So I took out the D_#__ in the taxonomic notation and the |__ notation. Once I did that, I was able to get the file to successfully run in galaxy.

I hope this helps, if it does not let me know!
Best,
Kelsey