LDA Effect Size (LEfSE) error

classic Classic list List threaded Threaded
1 message Options
| Threaded
Open this post in threaded view
|

LDA Effect Size (LEfSE) error

Caroline Kelsey
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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/