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I understand that people use Games Howell, Tukey or sometimes pair-wise t-test (with correction) test as post hoc analysis procedures following one-way ANOVA.

My question is following. For example, I have four groups, A, B, C and D. I did a ANOVA and found a significant p-value. If I only care about A vs B, A vs C and C vs D, what post hoc analysis procedure do I need to use?

Thanks in advance.

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Whichever you like. Anything advertised as a post-hoc test for a one-way ANOVA will tell you about such pairwise relationships. The fact that you don't care about some of the pairs won't invalidate any of these methods.

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  • $\begingroup$ Thanks. How about repeated measured ANOVA? The only post-hoc I know is the pair-wise paired t-test with Bonferroni (or other similar) correction. Suppose I have to use repeated ANOVA and I have, say 20 repeated measured groups but I only care the 1st group against other 19 groups. Would you recommend me to use pair-wise paired t-test with Bonferroni correction on all-comparison or just on 1st-rest compairson? $\endgroup$
    – WCMC
    Commented Jul 3, 2017 at 3:10
  • $\begingroup$ @WCMC If you're using a Bonferroni (or, better, Holm-Bonferroni) correction, then you do need to use it for every comparison you're looking at. This said, if you're using (Holm-)Bonferroni-corrected $t$-tests on pairs, and all you care about is the pairwise differences, there's no need to do the ANOVA itself. $\endgroup$
    – Kodiologist
    Commented Jul 3, 2017 at 3:20
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    $\begingroup$ Hi @Kodiologist, maybe I was unclear. For example I have 20 repeated measured groups. If I only care the 1st group vs 2nd, 1st group vs 3rd, 1st group vs 4th, ..., 1st group vs 20th, should I use pair-wise paired t-test with Holm correction on these 20 comparisons or on all-compairsons (1 vs 2, ..., 1vs20, 2vs3,...,2vs20, ..., 19vs20)? From your answer, I think on 20 comparisons was better? $\endgroup$
    – WCMC
    Commented Jul 3, 2017 at 3:28
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    $\begingroup$ Surely the choice has a power implication? I.e. even if any valid test will be valud, some may be better choices? $\endgroup$
    – Björn
    Commented Jul 3, 2017 at 5:50
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    $\begingroup$ You wouldn't want to make any adjustment for comparisons you didn't make. Some canned tests have been developed for common situations - e.g. Dunnett's control vs treatments test & Hsu's best vs rest test - or you can use Bonferroni adjustment for just the comparisons you make. $\endgroup$
    – Scortchi - Reinstate Monica ♦
    Commented Jul 3, 2017 at 11:22

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