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multcompare and ttest2

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karlo gonzales
karlo gonzales on 2 Mar 2016
Dear Friends,
I have a simple and very basic question regarding the P-value of multcompare and ttest2 function. As i understand, after anova we use PostHoc analysis to p-value between all pairs. I expected to have the same p-value using ttest2. BUT, their p-value is very different! would you please to help me to figure out the problem? thanks Karlo

Answers (1)

the cyclist
the cyclist on 2 Mar 2016
Edited: the cyclist on 2 Mar 2016
When you make pairwise comparisons among several groups (not just two), you are more likely to find a difference between a given pair, just by random chance.
The P-values you get from multcompare take into account. The P-values you get from running all the t-tests independently does not (because it doesn't "know" that you have run multiple comparisons.)
  5 Comments
Felix-Antoine Savoie
Felix-Antoine Savoie on 21 Jan 2019
Dear the cyclist,
You are correct that uncorrected multiple comparisons may lead to false positives (by chance). However, when using "multcompare" with the 'lsd' correction i(e, non-corrected ttest), I still get p-values that differ from those obtained from a standard ttest (not very different, but still). Do you have any idea as to why this happens?
Felix

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