Doh! You are, of course, correct. Thansk again for the help it is working
fine now.
The rpy2 way looks a lot nicer than the horrible hacks I'm writing now
though, so I guess I should make the effor to start using that and convert
all mu old codes.
Thanks again!
Nick
On 7 October 2011 14:37, Laurent Gautier <lgaut...@gmail.com> wrote:
> **
> Did you terminate your session and restarted ?
> If not, it won't work until you clear "estimateVarianceFunction" from the
> current R GlobalEnv.
>
>
> L.
>
>
>
>
> On 2011-10-07 15:33, Nick Schurch wrote:
>
> Thanks for the swift replies!
>
> I've tried renaming the function and running things again and unfortunately
> this doesn't solve the problem.
>
> So:
>
> r('testVarFunc <-
> function(rdata){x=estimateVarianceFunctions(rdata)\nstr(x)\nreturn(x)}')
>
> returns exactly the same error. Unfortunately at the moment I'm stuck using
> rpy v1 until rpy2 gets installed on our cluster. Could it be a problem with
> using rpy rather than rpy2?
>
> Nick
>
>
> On 7 October 2011 12:57, Laurent Gautier <lgaut...@gmail.com> wrote:
>
>> On 2011-10-07 13:05, Thomas Kluyver wrote:
>>
>> On 7 October 2011 11:57, Nick Schurch <n.schu...@dundee.ac.uk> wrote:
>>
>>> 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=)?
>>>
>>
>> By giving your function the same name as the function from the library, I
>> assume you're overriding it. This would mean your function calls itself
>> instead of the library function, and recurses infinitely.
>>
>>
>> Thomas' intuition about an infinite recursion is correct. The R statement
>> is creating a copy in the search path found before the one from the package
>> DESeq.
>> There is a bit of documentation about that at:
>>
>> http://rpy.sourceforge.net/rpy2/doc-2.2/html/rinterface.html#sexpenvironment
>>
>>
>> Why not call your function something else (even just
>> "myEstimateVarianceFunctions" or "wrapperEstimateVarianceFunctions")?
>>
>>
>> There is also some demo code to use related Bioconductor code (edgeR). By
>> chronological order:
>> -
>> http://bcbio.wordpress.com/2009/09/13/differential-expression-analysis-with-bioconductor-and-python/
>> - http://www.biomedcentral.com/1471-2105/11/S12/S11
>>
>> Statements like the one just below can be confusing and error-prone,
>> obviously.
>>
>> r('estimateVarianceFunctions <-
>> function(){load("mySavedR.rdata")\nx=estimateVarianceFunctions(z)\nreturn(x)}')
>>
>>
>> Consider replacing it with:
>>
>> from rpy2.robjects.packages import importr
>> base = importr('base')
>> deseq = importr('DESeq')
>> def estimate_variance(rdata_filename = "mySaveR.rdata"):
>> my_env = base.new_env()
>> # keep R's GlobalEnv clean (and avoid overwriting elements)
>> base.load(rdata_filename, envir = my_env)
>> return deseq.estimateVarianceFunction(my_env['z'])
>>
>> estimate_variance()
>>
>>
>>
>>
>> Thomas
>>
>>
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.http://p.sf.net/sfu/splunk-d2dcopy2
>>
>>
>> _______________________________________________
>> rpy-list mailing
>> listrpy-list@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rpy-list
>>
>>
>>
>
>
> --
> 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
>
> --
> 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
> <%2B44%201382%20345%20893>
>
>
------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
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