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Contrasts in mixed ANOVA

Dear all,

I need help to explain the contrasts in ANOVA.

I have run a two-ways mixed anova (A = the within factor and B = the between factor). I have a main effect for A then B separately. I have also an interaction A*B.

To avoid the multiple comparisons in post hoc for the interaction A*B (due to a low number of subjects), I have performed custom contrasts based on my planned hypothesis. But, I don't understand the test that is performed in JASP, it's a T test ? I don't think so because I compared and it is not the same results...

If someone has the answer ? let me know ;-)

Thanks very much for any advice!


  • Hi RobinM,

    The contrast analysis and post hoc tests basically conduct t-tests on the subsets of your data (comparing one group to another, based on 1 or more categorical variables). For an example, see the attached screenshot:

    We select all observations in group 3 of the variable facFive in the group Level.1 in RM Factor 1, and we compare those to the observations in group 5 of facFive in the group Level.1 in RM Factor 1.

    since these observations are between subjects, the t-test conducted here is a two-sample t-test (with a different error term and therefore p-value). If you were to compare groups between the levels of the RM factor, this would be a paired samples t-test, so maybe that's where your results are different?

    For an overview of posthoc tests, contrasts, and marginal means, see also my blogpost on the topic here:

    I hope this helps, please let me know if you have additional questions =)

    Kind regards,


  • Dear Johnny,

    Thank you for you answer.

    I actually have a two groups (gender as between factor -> women or men) and five repeated-measures (time). My data set includes 10 women and 8 men.

    Please find attached screenshot with the contrast result comparing women vs men for the time noted "POST" and in comparison, the two-sample t-test.

    The results are not the same beacause like you said, there is a different error term, but I don't understand how is computed this error ? The degrees of freedom are different, how is it calculated for the contrasts ?

    I have already seen your blogpost and it helped me a lot ;-)

    Thank you again !

    Have a nice day


  • Hi Robin,

    Im afraid I am not entirely sure how these are calculated. All I can say is that in the contrast analysis, the comparisons are conducted as one whole, which means that there are more groups being considered than just the 2 groups that are shown in the individual t-test, which leads to a higher degrees of freedom. Furthermore, there is pooling of the standard deviations across all these different groups.

    I think this paper can shed some light on it, if you want to read about it further.

    Kind regards


  • Okay no worries.

    The simple fact that the contrasts consider more than 2 groups (in term of error) is really interesting and comforts me that these analyses are really well adapted to answer planned questions and so to avoid multiple comparisons.

    Thank you


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