Hi, Ted and Dennis:
 
Thanks for your speedy replies!  I don't think this happens just randomly, rather, I'm thinking it may be due to the way chisq.test function handles simulation.  Here shows why: (Ted, I think there is an error in your code, "tx" should be t(x)  )

> x
     [,1] [,2]
[1,]  149  151
[2,]    1    8
> c2x<-chisq.test(x, simulate.p.value=T, B=100000)$p.value
> for(i in (1:20)){c2x<-c(c2x,chisq.test(x, simulate.p.value=T,
+                        B=100000)$p.value)}
> c2tx<-chisq.test(t(x), simulate.p.value=T, B=100000)$p.value
> for(i in (1:20)){c2tx<-c(c2tx,chisq.test(t(x), simulate.p.value=T,
+                         B=100000)$p.value)}
> cbind(c2x,c2tx)
          c2x    c2tx
 [1,] 0.03727 0.01629
 [2,] 0.03682 0.01662
 [3,] 0.03671 0.01665
 [4,] 0.03788 0.01745
 [5,] 0.03706 0.01646
 [6,] 0.03715 0.01728
 [7,] 0.03664 0.01683
 [8,] 0.03681 0.01720
 [9,] 0.03742 0.01758
[10,] 0.03712 0.01685
[11,] 0.03739 0.01615
[12,] 0.03811 0.01653
[13,] 0.03711 0.01673
[14,] 0.03639 0.01678
[15,] 0.03714 0.01719
[16,] 0.03774 0.01780
[17,] 0.03574 0.01707
[18,] 0.03661 0.01705
[19,] 0.03751 0.01711
[20,] 0.03683 0.01718
[21,] 0.03678 0.01653
 
 
 
...Tao
 
============================================================
Ted.Harding@nessie.mcc.ac.uk wrote:
On 15-Jul-03 Tao Shi wrote:
>>x
> [,1] [,2]
> [1,] 149 151
> [2,] 1 8
>>t(x)
> [,1] [,2]
> [1,] 149 1
> [2,] 151 8
>>chisq.test(x, simulate.p.value=T, B=100000)
> Pearson's Chi-squared test with simulated p-value (based on
> 1e+05 replicates)
> data: x
> X-squared = 5.2001, df = NA, p-value = 0.03774
> 
>>chisq.test(t(x), simulate.p.value=T, B=100000)
> Pearson's Chi-squared test with simulated p-value (based on
> 1e+05 replicates)
> data: t(x)
> X-squared = 5.2001, df = NA, p-value = 0.01642

Possibly you may just have been unlucky, though the 0.03774 seems large:

c2x<-chisq.test(x, simulate.p.value=T, B=100000)$p.value
for(i in (1:9)){c2x<-c(c2x,chisq.test(x, simulate.p.value=T,
B=100000)$p.value)}
c2tx<-chisq.test(tx, simulate.p.value=T, B=100000)$p.value
for(i in (1:9)){c2tx<-c(c2tx,chisq.test(tx, simulate.p.value=T,
B=100000)$p.value)}
cbind(c2x,c2tx)
c2x c2tx
[1,] 0.01627 0.01720
[2,] 0.01672 0.01690
[3,] 0.01662 0.01669
[4,] 0.01733 0.01656
[5,] 0.01679 0.01777
[6,] 0.01715 0.01769
[7,] 0.01765 0.01769
[8,] 0.01703 0.01740
[9,] 0.01704 0.01708
[10,] 0.01669 0.01655

sd(c2x)
[1] 0.0003946715
sd(c2tx)
[1] 0.0004737099

Ted.


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E-Mail: (Ted Harding) 
Fax-to-email: +44 (0)870 167 1972
Date: 15-Jul-03 Time: 21:00:04
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