R help - Nov 2009 - fisher.test negative value error

Hi all,

I am new to python, R and rpy2. I having few errors when I am using
'fisher.test' function where I am struck now. Please help to fix these
bugs.
My code for fisher.test goes this way

*from rpy2 import *
import rpy2.robjects as robjects
def fisherExact(a,b,c,d):
   v = [a,b,c,d]
   m = robjects.r['matrix'](v,2,2)
   s = robjects.r['fisher.test'](m)
   return s
*

Here the value of a=0,b=1,c=0 and d=1. so the matrix m should be like this

     [,1] [,2]
[1,] 0    0
[2,] 1    1

But I am getting an error like this

*File "/usr/lib64/python2.6/site-packages/rpy2/robjects/__init__.py",
line
422, in __call__
    res = super(RFunction, self).__call__(*new_args, **new_kwargs)
rinterface.RRuntimeError: Error in function (x, y = NULL, workspace = 2e+05,
hybrid = FALSE, control = list(),  :
  all entries of 'x' must be nonnegative and finite*

clearly every element of matrix m is +ve but I don't know why I am getting
this error. I am using python 2.6,R-core-2.9.2-1 and rpy2.

Please help me in this regard.

Thanks,
Bhanu.

	[[alternative HTML version deleted]]

> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Bhanu Mangipudi
> Sent: Wednesday, November 11, 2009 11:16 AM
> To: r-help at r-project.org
> Subject: [R] fisher.test negative value error
> 
> Hi all,
> 
> I am new to python, R and rpy2. I having few errors when I am using
> 'fisher.test' function where I am struck now. Please help to 
> fix these bugs.
> My code for fisher.test goes this way
> 
> *from rpy2 import *
> import rpy2.robjects as robjects
> def fisherExact(a,b,c,d):
>    v = [a,b,c,d]
>    m = robjects.r['matrix'](v,2,2)
>    s = robjects.r['fisher.test'](m)
>    return s
> *
> 
> Here the value of a=0,b=1,c=0 and d=1. so the matrix m should 
> be like this
> 
>      [,1] [,2]
> [1,] 0    0
> [2,] 1    1
> 
> But I am getting an error like this
> 
> *File 
> "/usr/lib64/python2.6/site-packages/rpy2/robjects/__init__.py",
line
> 422, in __call__
>     res = super(RFunction, self).__call__(*new_args, **new_kwargs)
> rinterface.RRuntimeError: Error in function (x, y = NULL, 
> workspace = 2e+05,
> hybrid = FALSE, control = list(),  :
>   all entries of 'x' must be nonnegative and finite*
I think you are passing a list matrix to fisher.test, not
a numeric matrix.  E.g.,
  > fisher.test(matrix(list(0,1,0,1),2,2))
  Error in fisher.test(matrix(list(0, 1, 0, 1), 2, 2)) : 
    all entries of 'x' must be nonnegative and finite
The python v should be a numeric array instead of a list.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com  

> 
> clearly every element of matrix m is +ve but I don't know why 
> I am getting
> this error. I am using python 2.6,R-core-2.9.2-1 and rpy2.
> 
> Please help me in this regard.
> 
> Thanks,
> Bhanu.
> 
> 	[[alternative HTML version deleted]]
> 
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