Re: [Rpy] Problems with DESeq library in rpy

2011-10-07 Thread Laurent Gautier
May be with deseq.estimateVarianceFunctions ? On 2011-10-07 16:09, Nick Schurch wrote: 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

Re: [Rpy] Problems with DESeq library in rpy

2011-10-07 Thread Nick Schurch
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. (

Re: [Rpy] Problems with DESeq library in rpy

2011-10-07 Thread Nick Schurch
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, Lau

Re: [Rpy] Problems with DESeq library in rpy

2011-10-07 Thread Laurent Gautier
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 unfortunat

Re: [Rpy] Problems with DESeq library in rpy

2011-10-07 Thread Laurent Gautier
On 2011-10-07 13:05, Thomas Kluyver wrote: On 7 October 2011 11:57, Nick Schurch > wrote: r('estimateVarianceFunctions <- function(){load("mySavedR.rdata")\nx=estimateVarianceFunctions(z)\nreturn(x)}') and then call it from python: >>> test = r.e

Re: [Rpy] Problems with DESeq library in rpy

2011-10-07 Thread Thomas Kluyver
On 7 October 2011 11:57, Nick Schurch 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): > Fil

[Rpy] Problems with DESeq library in rpy

2011-10-07 Thread Nick Schurch
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=estimateVarianceFuncti