The bioBakery help forum

LDA effect size (lefse) error: all observations are in the same group

Hello everyone
/galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/init.py:185: RRuntimeWarning: Error in kruskal.test.default(c(0, 0, 467.164975974373, 0, 0, 0, 0, 0, :
all observations are in the same group

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 67, in
kw_ok,pv = test_kw_r(cls,feat_values,params[‘anova_alpha’],sorted(cls.keys()))
File “/export/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/lefse.py”, line 59, in test_kw_r
kw_res = robjects.r(‘kruskal.test(’+fo+’,)$p.value’)
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 kruskal.test.default(c(0, 0, 467.164975974373, 0, 0, 0, 0, 0, :
all observations are in the same group

can someone please help
Thanks

Hello,
I’m wondering if there’s an issue with how the class variable is being specified–do you have an example dataset you could send and I can try to troubleshoot?
Best,
Meg