[R] Fisher test problem
Viju Moses
vijumoses at gmail.com
Sun Mar 22 07:39:53 CET 2009
As you say, I guess that's not possible. Meanwhile I've got R's results verified in Stata
. tabi 17 6 \ 2 1, chi2 exact
| col
row | 1 2 | Total
-----------+----------------------+----------
1 | 17 6 | 23
2 | 2 1 | 3
-----------+----------------------+----------
Total | 19 7 | 26
Pearson chi2(1) = 0.0708 Pr = 0.790
Fisher's exact = 1.000
1-sided Fisher's exact = 0.627
The OpenEpi.com output was: (note the 2 tailed P value (fisher test))
Chi Square and Exact Measures of Association
Test Value p-value(1-tail) p-value(2-tail)
Uncorrected chi square 0.07083 0.3951 0.7901
Yates corrected chi square 0.1813 0.3351 0.6702
Mantel-Haenszel chi square 0.06811 0.3971 0.7941
Fisher exact 0.6273 1.25
Mid-P exact 0.3971 0.7942
Thanks for pointing it out.. Had been under the notion that OpenEpi was very... strong (being associated with EpiInfo and WHO).
Viju
Tal Galili wrote:
> Viju Moses,
> Are you sure you got a P-value of 1.25 ?
> Since P-value could only be between 0 to 1...
>
> Tal
>
>
>
>
>
> On Sat, Mar 21, 2009 at 9:17 PM, Viju Moses <vijumoses at gmail.com
> <mailto:vijumoses at gmail.com>> wrote:
>
> Hi, I noted a discrepancy between R and openepi when I ran a fisher
> test with the same matrix. In R:
>
> > a=matrix(c(1,2,6,17), nrow=2)
> > a
> [,1] [,2]
> [1,] 1 6
> [2,] 2 17
> > fisher.test(a, conf.int <http://conf.int>=T)
>
> Fisher's Exact Test for Count Data
>
> data: a
> p-value = 1
> alternative hypothesis: true odds ratio is not equal to 1
> 95 percent confidence interval:
> 0.02061498 31.73691924
> sample estimates:
> odds ratio
> 1.396646
>
> But in openepi the P value is 1.25. (In another instance too for
> other sets of data, I had got a p value of 1 in 3 instances for a
> prop.test when I got 3 other answers on a friend's stata software
> with the same data. )
>
> I'm using R on Ubuntu Intrepid. Is there anything I'm doing wrong?
> Any other packages I have to install?
>
> Thanks in advance
>
> Viju Moses
>
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>
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