[R] pairwise.t.test vs. t. test

[Peter Dalgaard]

"MARK LEEDS" <markleeds at verizon.net> writes:

> thanks. i assumed we we were talking about the standard textbook difference 
> between the t test and pairwise t test.
> my bad.

Notice the difference between paired and pairwise...


> ----- Original Message ----- 
> From: "Chuck Cleland" <ccleland at optonline.net>
> To: "MARK LEEDS" <markleeds at verizon.net>
> Cc: "Li,Qinghong,ST.LOUIS,Molecular Biology" <Qinghong.Li at rdmo.nestle.com>; 
> <r-help at stat.math.ethz.ch>
> Sent: Thursday, September 07, 2006 6:44 PM
> Subject: Re: [R] pairwise.t.test vs. t. test
> 
> 
> > MARK LEEDS wrote:
> >> no, because the formula for the test statistics ( even assuming that
> >> variances are equal ) of the two different tests are different. in the
> >> pairwise t test, the pairwise differences are
> >> viewed as one sample so it turns into a one sample test. any intro stat 
> >> book
> >> will have the formulas.
> >>
> >>      mark
> >
> >  Actually, I think the difference is due to the SD being pooled across
> > all 3 groups in the pairwise.t.test, but just 2 groups in t.test.
> >
> >> ----- Original Message ----- 
> >> From: "Li,Qinghong,ST.LOUIS,Molecular Biology" 
> >> <Qinghong.Li at rdmo.nestle.com>
> >> To: <r-help at stat.math.ethz.ch>
> >> Sent: Thursday, September 07, 2006 5:07 PM
> >> Subject: [R] pairwise.t.test vs. t. test
> >>
> >>
> >>> Hi,
> >>>
> >>> If I set the p.adjust="none", does it meant that the output p values 
> >>> from
> >>> the pairwise.t.test will be the same as those from individual t.tests 
> >>> (set
> >>> var.equal=T, alternative="t")?
> >>>
> >>> I actually got different p values from the two tests. See below. Is it
> >>> supposed to be this way?
> >>>
> >>> Thanks
> >>> Johnny
> >>>
> >>>> x
> >>> [1] 61.6 52.7 61.3 65.2 62.8 63.7 64.8 58.7 44.9 57.0 64.3 55.1 50.0 
> >>> 41.0
> >>> [15] 43.0 45.9 52.2 45.5 46.9 31.6 40.6 44.8 39.4 31.0 37.5 32.6 23.2 
> >>> 34.6
> >>> [29] 38.3 38.1 19.5 21.2 15.8 33.3 28.6 25.8
> >>>> Grp
> >>> [1] Yng Yng Yng Yng Yng Yng Yng Yng Yng Yng Yng Yng Med Med Med Med Med
> >>> Med
> >>> [19] Med Med Med Med Med Med Old Old Old Old Old Old Old Old Old Old Old
> >>> Old
> >>> Levels: Yng Med Old
> >>>>  pairwise.t.test(x=x,g=Grp,p.adjust.method="none")
> >>>        Pairwise comparisons using t tests with pooled SD
> >>>
> >>> data:  x and Grp
> >>>
> >>>    Yng     Med
> >>> Med 1.0e-06 -
> >>> Old 2.0e-12 2.6e-05
> >>>
> >>> P value adjustment method: none
> >>>
> >>>
> >>>> t.test(x=x[1:12],y=x[25:36],var.equal=T, alternative="t")
> >>>        Two Sample t-test
> >>>
> >>> data:  x[1:12] and x[25:36]
> >>> t = 10.5986, df = 22, p-value = 4.149e-10
> >>> alternative hypothesis: true difference in means is not equal to 0
> >>> 95 percent confidence interval:
> >>> 24.37106 36.22894
> >>> sample estimates:
> >>> mean of x mean of y
> >>> 59.34167  29.04167
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> ______________________________________________
> >>> R-help at stat.math.ethz.ch mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>> PLEASE do read the posting guide
> >>> http://www.R-project.org/posting-guide.html
> >>> and provide commented, minimal, self-contained, reproducible code.
> >>>
> >>
> >> ______________________________________________
> >> R-help at stat.math.ethz.ch mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide 
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > -- 
> > Chuck Cleland, Ph.D.
> > NDRI, Inc.
> > 71 West 23rd Street, 8th floor
> > New York, NY 10010
> > tel: (212) 845-4495 (Tu, Th)
> > tel: (732) 512-0171 (M, W, F)
> > fax: (917) 438-0894
> >
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
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