on a related matter, I've put a local install of pyr2 on my machine (also
running R2.12.1) and tried the script you suggested:
Python 2.6.4 (r264:75706, Sep 10 2010, 16:37:14)
[GCC 4.1.2 20071124 (Red Hat 4.1.2-42)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
(InteractiveConsole)
>>> from rpy2.robjects.packages import importr
>>> base = importr('base')
>>> deseq = importr('DESeq')
locfit 1.5-6 2010-01-20
>>> my_env = base.new_env()
>>> rdata_filename = "mydata.Rdata"
>>> base.load(rdata_filename, envir = my_env)
<StrVector - Python:0x7ba1998 / R:0x8a0c4c8>
['z']
>>> deseq.estimateVarianceFunction(my_env['z'])
Traceback (most recent call last):
File "<console>", line 1, in <module>
AttributeError: 'SignatureTranslatedPackage' object has no attribute
'estimateVarianceFunction'
>>>
I'm not sure why its doing this, but I don't thing importr('DESeq') is
loading everything it needs. Under rpy v1 I was using
>>> r.library("DESeq")
Loading required package: locfit
Loading required package: akima
Loading required package: lattice
locfit 1.5-6 2010-01-20
c.f.
>>> deseq = importr('DESeq')
locfit 1.5-6 2010-01-20
any ideas?
Nick
On 7 October 2011 14:46, Nick Schurch <n.schu...@dundee.ac.uk> wrote:
> 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
>>>
>>>
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>>> 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
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>>>
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>>> rpy-list mailing
>>> listrpy-list@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rpy-list
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>>>
>>>
>>
>>
>> --
>> 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>
>>
>>
--
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
------------------------------------------------------------------------------
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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