> -----Original Message-----
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of Bhanu Mangipudi
> Sent: Wednesday, November 11, 2009 11:16 AM
> To: r-help@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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