On Sep 10, 2010, at 9:01 AM, Jabez Wilson wrote:
> Dear all, I am perplexed when trying to get the same results using
> pairwise.t.test and t.test.
> I'm using examples in the ISwR library,
>> attach(red.cell.folate)
> I can get the same result for pairwise.t.test and t.test when I set the
> variances to be non-equal, but not when they are assumed to be equal. Can
> anyone explain the differences, or what I'm doing wrong?
> Here's an example where I compare the first two ventilations with
> pairwise.t.test and t.test
>> pairwise.t.test(folate, ventilation, p.adj="none", pool.sd=F)
> Pairwise comparisons using t tests with non-pooled SD
> data: folate and ventilation
> N2O+O2,24h N2O+O2,op
> N2O+O2,op 0.029 -
> O2,24h 0.161 0.298
> P value adjustment method: none
>
>> t.test(folate[1:8], folate[9:17], var.equal=F)
> Welch Two Sample t-test
> data: folate[1:8] and folate[9:17]
> t = 2.4901, df = 11.579, p-value = 0.02906
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> 7.310453 113.050658
> sample estimates:
> mean of x mean of y
> 316.6250 256.4444
>
> So 0.029 and 0.02906 are identical but if I do the same with pool.sd and
> var.equal = T, I get different results
>> pairwise.t.test(folate, ventilation, p.adj="none", pool.sd=T)
> Pairwise comparisons using t tests with pooled SD
> data: folate and ventilation
> N2O+O2,24h N2O+O2,op
> N2O+O2,op 0.014 -
> O2,24h 0.155 0.408
> P value adjustment method: none
>
>> t.test(folate[1:8], folate[9:17], var.equal=T)
> Two Sample t-test
> data: folate[1:8] and folate[9:17]
> t = 2.5582, df = 15, p-value = 0.02184
> alternative hypothesis: true difference in means is not equal to 0
> 95 percent confidence interval:
> 10.03871 110.32240
> sample estimates:
> mean of x mean of y
> 316.6250 256.4444
>
> So 0.014 and 0.02184 are not the same.
>
require(ISwR)
> with(red.cell.folate[1:17, ], pairwise.t.test(folate, ventilation, pool.sd =
> TRUE))$p.value
N2O+O2,24h
N2O+O2,op 0.02184081
NB: The pool.SD switch calculates a common SD for all groups and used that for
all comparisons
See the Details in ?pairwise.t.test
HTH,
Marc Schwartz
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