dear Rpyers,
I'm having some problems using parts of the DESeq library from rpy,
specifically when I try to use theestimateVarianceFunctions function.
I have a saved R CountDataSet object. If I load this object in R (as
variable z), load the DESeq library and then run:
> x=estimateVarianceFunctions(z)
it works just fine.
if however I import rpy, load the DESeq library, define the following
bespoke rpy function
r('estimateVarianceFunctions <-
function(){load("mySavedR.rdata")\nx=estimateVarianceFunctions(z)\nreturn(x)}')
and then call it from python:
>>> test = r.estimateVarianceFunctions()
I get:
Traceback (most recent call last):
File "<console>", line 1, in <module>
RPy_RException: Error: evaluation nested too deeply: infinite recursion /
options(expressions=)?
I have no idea why its doing this - its executing exactly the same R
commands, using exactly the same version of R (2.13.1) and exactly the same
version of the DESeq library (1.4.1) on the same machine.
Any help would be gratefully appreciated....
--
Cheers,
Nick Schurch
Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK
Tel: +44 1382 388707
Fax: +44 1382 345 893
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