Hello,
First of all thank you for all of your hard work developing such an
informative and intuitive tool. I have been successful in running the LEfSE
analyses for some of my data, but unfortunately, for the majority I get an
error message when it comes to the step where the Effect size is
calculated. The error message is copied below:
/galaxy_venv/local/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:185:
RRuntimeWarning: Error in (function (file = "", n = NULL, text = NULL,
prompt = "?", keep.source = getOption("keep.source"), :
<text>:1:47: unexpected numeric constant
1: effect.size <- abs(mean(LD[sub_d[,"class"]==""1
^
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 199, in test_lda_r
robjects.r('effect.size <-
abs(mean(LD[sub_d[,"class"]=="'+p[0]+'"]) -
mean(LD[sub_d[,"class"]=="'+p[1]+'"]))')
File
"/galaxy_venv/local/lib/python2.7/site-packages/rpy2/robjects/__init__.py",
line 358, in __call__
p = _rparse(text=StrSexpVector((string,)))
rpy2.rinterface.RRuntimeError: Error in (function (file = "", n =
NULL, text = NULL, prompt = "?", keep.source =
getOption("keep.source"), :
<text>:1:47: unexpected numeric constant
1: effect.size <- abs(mean(LD[sub_d[,"class"]==""1
^
For your reference, I am using this tool to analyze human gut microbiome
data.
Also, I cross-posted to the forum (link:
https://help.galaxyproject.org/t/lda-effect-size-error/2840)
Any guidance would be greatly appreciated.
all the best,
Caroline
--
Caroline M. Kelsey
Developmental Psychology Ph.D. Candidate
UVA Babylab: http://uvababylab.org/
The University of Virginia
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