# Re: [R] Chi-Square Test Disagreement

From: Berwin A Turlach <berwin_at_maths.uwa.edu.au>
Date: Thu, 27 Nov 2008 00:46:31 +0800

G'day Andy,

On Wed, 26 Nov 2008 14:51:50 +0000
Andrew Choens <andy.choens_at_gmail.com> wrote:

> I was asked by my boss to do an analysis on a large data set, and I am
> trying to convince him to let me use R rather than SPSS.

Very laudable of you. :)

> This is the output from R:
> > chisq.test(test29)
>
> Pearson's Chi-squared test
>
> data: test29
> X-squared = 9.593, df = 4, p-value = 0.04787
>
> But, the same data in SPSS generates a p value of .051. It's a small
> but important difference.

> I played around and rescaled things, and tried different values for
> B, but I never could get R to reach .051.

Well, I have no problem when using simulated p-values to get something close to 0.051; look at the last try. The second one might also be noteworthy. Unfortunately, I didn't save the seed beforehand.

> test29 <- matrix(c(110,358,71,312,29,139,31,77,13,32), byrow=TRUE,
> ncol=2) test29

[,1] [,2]

```[1,]  110  358
[2,]   71  312
[3,]   29  139
[4,]   31   77
[5,]   13   32
```

> chisq.test(test29, simul=TRUE)
```	Pearson's Chi-squared test with simulated p-value (based on 2000
replicates)

```

data: test29
X-squared = 9.593, df = NA, p-value = 0.04798

```	Pearson's Chi-squared test with simulated p-value (based on 2000
replicates)

```

data: test29
X-squared = 9.593, df = NA, p-value = 0.05697

> chisq.test(test29, simul=TRUE, B=20000)

Pearson's Chi-squared test with simulated p-value (based on 20000 replicates)

data: test29
X-squared = 9.593, df = NA, p-value = 0.0463

> chisq.test(test29, simul=TRUE, B=20000)

Pearson's Chi-squared test with simulated p-value (based on 20000 replicates)

data: test29
X-squared = 9.593, df = NA, p-value = 0.0499

> chisq.test(test29, simul=TRUE, B=20000)

Pearson's Chi-squared test with simulated p-value (based on 20000 replicates)

data: test29
X-squared = 9.593, df = NA, p-value = 0.0486

> chisq.test(test29, simul=TRUE, B=20000)

Pearson's Chi-squared test with simulated p-value (based on 20000 replicates)

data: test29
X-squared = 9.593, df = NA, p-value = 0.05125

Cheers,

Berwin

• Full address ============================= Berwin A Turlach Tel.: +65 6516 4416 (secr) Dept of Statistics and Applied Probability +65 6516 6650 (self) Faculty of Science FAX : +65 6872 3919 National University of Singapore 6 Science Drive 2, Blk S16, Level 7 e-mail: statba_at_nus.edu.sg Singapore 117546 http://www.stat.nus.edu.sg/~statba

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