I am analysis with microbial data
when I run run_lefse.py data.in data.res
it has following error:
/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: Error in lda.default(x, grouping, …) :
variables 1 2 3 4 5 6 appear to be constant within groups
res = super(Function, self).__call__(*new_args, **new_kwargs)
Traceback (most recent call last):
File “/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/bin/run_lefse.py”, line 89, in
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 “/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/bin/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 “/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/lib/python2.7/site-packages/rpy2/robjects/init.py”, line 321, in call
res = self.eval(p)
File “/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/lib/python2.7/site-packages/rpy2/robjects/functions.py”, line 178, in call
return super(SignatureTranslatedFunction, self).call(*args, **kwargs)
File “/home/linuxbrew/.linuxbrew/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/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 lda.default(x, grouping, …) :
variables 1 2 3 4 5 6 appear to be constant within groups
how can I deal with it?