Dear R-help, I have a question about pairwise.t.test and adjustment for
multiple comparisons for paired data points.
I have the following data:
n=c("x", "x", "x", "x", "x",
"x", "x", "x", "x", "x",
"y", "y",
"y", "y", "y", "y", "y",
"y", "y", "y", "z", "z",
"z", "z", "z",
"z", "z", "z", "z", "z")
and
d=c(3.38501220258169, 0.732526675324789, -0.638736410843593,
7.87414894080545,
3.6341475242877, -2.80762187242111, 14.1405912463741, -9.29904247482419,
9.8636915453275, 5.43287495347734, 12.2804612051493, 7.83975161028828,
15.2200332220459, 6.72953902619773, 9.11557944514228, 9.79268012944973,
7.6112143261283, 10.3912598689021, 8.04934992955112, 13.3935024789408,
12.1276080143311, 11.2987640203845, 2.05386456839974, 12.8386335687123,
3.84418682233211, 17.4626505871045, 6.5947625121599, -10.6664750811034,
21.3346023277454, 4.99216977422232)
Then I do the tests
> pairwise.t.test(d,n,p.adjust="bonf",paired=F)
Pairwise comparisons using t tests with pooled SD
data: d and n
x y
y 0.092 -
z 0.326 1.000
P value adjustment method: bonferroni
Assuming the data are paired:
> pairwise.t.test(d,n,p.adjust="bonf",paired=T)
Pairwise comparisons using t tests with pooled SD
data: d and n
x y
y 0.092 -
z 0.326 1.000
P value adjustment method: bonferroni
I have no indication that the test is taking into account that the data are
paired! Is it possible to do a pairwise t test with adjustement for multiple
comparisons using pairwise.t.test? If not any other function for that?
Thanks.
--
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francogrex wrote:> Dear R-help, I have a question about pairwise.t.test and adjustment for > multiple comparisons for paired data points. > I have the following data: > > n=c("x", "x", "x", "x", "x", "x", "x", "x", "x", "x", "y", "y", > "y", "y", "y", "y", "y", "y", "y", "y", "z", "z", "z", "z", "z", > "z", "z", "z", "z", "z") > > and > > d=c(3.38501220258169, 0.732526675324789, -0.638736410843593, > 7.87414894080545, > 3.6341475242877, -2.80762187242111, 14.1405912463741, -9.29904247482419, > 9.8636915453275, 5.43287495347734, 12.2804612051493, 7.83975161028828, > 15.2200332220459, 6.72953902619773, 9.11557944514228, 9.79268012944973, > 7.6112143261283, 10.3912598689021, 8.04934992955112, 13.3935024789408, > 12.1276080143311, 11.2987640203845, 2.05386456839974, 12.8386335687123, > 3.84418682233211, 17.4626505871045, 6.5947625121599, -10.6664750811034, > 21.3346023277454, 4.99216977422232) > > Then I do the tests > > >> pairwise.t.test(d,n,p.adjust="bonf",paired=F) >> > > Pairwise comparisons using t tests with pooled SD > > data: d and n > > x y > y 0.092 - > z 0.326 1.000 > > P value adjustment method: bonferroni > > Assuming the data are paired: > > >> pairwise.t.test(d,n,p.adjust="bonf",paired=T) >> > > Pairwise comparisons using t tests with pooled SD > > data: d and n > > x y > y 0.092 - > z 0.326 1.000 > > P value adjustment method: bonferroni > > I have no indication that the test is taking into account that the data are > paired! Is it possible to do a pairwise t test with adjustement for multiple > comparisons using pairwise.t.test? If not any other function for that? > ThanksGet rid of the pooled SD, and pairwise.t.test() will actually do the paired tests, although that is not what the function was designed to do. (Oddly enough, this issue hasn't come up in the 6+ years that the function has existed, and then it pops up twice with little over a week between, see the thread started by James Root on March 26.) -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
francogrex wrote:> > <snipped>... > I have no indication that the test is taking into account that the data > are paired! Is it possible to do a pairwise t test with adjustement for > multiple comparisons using pairwise.t.test? If not any other function for > that? Thanks. >Dear all, Peter Dalgaard has pointed out to me that this topic was already discussed in a previous thread only about 2 weeks ago. Therefore please ignore my message above. Sorry for any inconveniance. Franco. -- View this message in context: http://www.nabble.com/pairwise.t.test-for-paired-data-tp16491877p16494840.html Sent from the R help mailing list archive at Nabble.com.