LDA Effect Size (LefSE) Error Message

[cmk6jm]

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"), :
: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
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"), :
: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

[bernt-matthias]

Replied on help.galaxyproject.org