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

**URL:** <https://forum.biobakery.org/t/b-lda-effect-size-lefse-error-please-help-me/1555>\
**Category:** LEfSe\
**Created:** [January 18, 2021, 9:28am UTC](https://forum.biobakery.org/t/b-lda-effect-size-lefse-error-please-help-me/1555 "2021-01-18T09:28:47Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![SJLim](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sjlim/32/577_2.png) [@SJLim](https://forum.biobakery.org/u/SJLim)\
**Post date:** [January 18, 2021, 9:28am UTC](https://forum.biobakery.org/t/b-lda-effect-size-lefse-error-please-help-me/1555/1 "2021-01-18T09:28:47Z")

</div>

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](https://forum.biobakery.org/uploads/short-url/6FoFyF7NzFksoM8sREV9Dsn7OWm.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'
```

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<div class="post-metadata">

**Author:** ![Kelsey\_Thompson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kelsey_thompson/32/65_2.png) [@Kelsey\_Thompson](https://forum.biobakery.org/u/Kelsey_Thompson)\
**Post date:** [January 21, 2021, 11:17pm UTC](https://forum.biobakery.org/t/b-lda-effect-size-lefse-error-please-help-me/1555/2 "2021-01-21T23:17:50Z")

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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