run_lefse.py , grouping , constant ,error

[xiaotian chen]

Hi,

I have an error when I run run_lefse.py  ,

the  format_lefse.txt is :

$ head -5  otu_table_lefse.txt

Treatment B1 B1 B3 B2 B2 B1 B3 B2

subject B1 B2 B3 B4 B5 B6 B7 B8

Archaea 0.00709823963657013 0.296411645226811 0.00532183506195859 0.317745409411163 0.0316011765593182 0.285696675843366 0.0913039980693428 0.00693469352666418

Archaea|Crenarchaeota 0.000496876774559909 0.00213270142180095 0.00143728392184283 0.00219034059796298 0.00414812580134248 0.0010683321691252 0.00211836001394364 0.00128950912685904

Archaea|Crenarchaeota|MBGA 0 0 7.76910228023152e-05 0.000474573796225313 0.000113130703672977 0 0.000134073418604028 0

python /home/test/LEfSE/format_input.py otu_table_lefse.txt format_lefse.txt -c 1 -o 1000000 -s -1 -u 2

 

python /home/test/LEfSE/run_lefse.py format_lefse.txt run_lefse.txt -y 1

Number of significantly discriminative features: 17 ( 31 ) before internal wilcoxon

/usr/lib64/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: Error in lda.default(x, grouping, ...) : 

  variables  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 appear to be constant within groups

  res = super(Function, self).__call__(*new_args, **new_kwargs)

Traceback (most recent call last):

  File "/home/test/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 "/home/test/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 "/usr/lib64/python2.7/site-packages/rpy2/robjects/__init__.py", line 311, in __call__

    res = self.eval(p)

  File "/usr/lib64/python2.7/site-packages/rpy2/robjects/functions.py", line 178, in __call__

    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)

  File "/usr/lib64/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  7  8  9 10 11 12 13 14 15 16 17 appear to be constant within groups

[xiaotian chen]

Is  anybody  encountered the same problem   ？

在 2016年4月29日星期五 UTC+8下午5:17:29，xiaotian chen写道：