Thanks for the hint. I found out how to specify contrasts in multcomp using
function contrMat:
https://stats.stackexchange.com/questions/104028/r-multcomp-contrasts-for-tukey
This is about Tukey's test, but the principle is the same for all tests

However, it seems that repeated t-tests with pooled variance are not
supported in multcomp:
http://www.inside-r.org/packages/cran/multcomp/docs/contrMat

Am I wrong? If not, how could I do repeated t-tests for specific contrasts?

Thank you
Andreas



On Wed, Jun 11, 2014 at 10:28 AM, ONKELINX, Thierry <
Thierry.ONKELINX@inbo.be> wrote:

> Have a look at the multcomp package. The examples in glht() demonstrate
> how to specify the required contrasts.
>
> Best regards,
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
> Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx@inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
>
> -----Oorspronkelijk bericht-----
> Van: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org]
> Namens Andreas Maunz
> Verzonden: woensdag 11 juni 2014 10:02
> Aan: r-help@r-project.org
> Onderwerp: [R] aov + pairwise.t.test: only selected pairs
>
> Hi,
>
> I have a 1-way anova result and want to do a post test.
>
> I want to do pairwise t-tests where the global variance is taken into
> account (i.e. a real post test on the anova result, not multiple simple t
> tests on the samples).
>
> I understand I should use pairwise.t.test() for that. However, it does not
> allow me to select specific pairs, it always analyzes all pairs. How can I
> analyze specific pairs only?
>
> Thanks
> Andreas
>
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