Does anyone know if JMP will give you MSD value (minimum significant difference) for a multiple comparison test (i.e. Tukey's HSD)? If so please let me know how to get it. THANKS!
The minimum significant difference is not the same for all pairwise comparisons unless the sample sizes for all groups are equal. When sample sizes are not equal, then the minimum significant difference will vary from comparison to comparison.
If you are using the Fit Y by X platform (Oneway Analysis), you can determine the minimum significant difference as described earlier. When you do the comparisons, you will get an LSD or HSD Threshold Matrix which is the absolute value fo the difference minus the LSD or HSD. From the red triangle menu, you can obtain the Difference Matrix. You can use these together to determine the LSD or HSD.
In the Fit Model platform, you will get a matrix of the LSMeans Differences for the multiple comparison method chosen. In that case the test statistic (Q for Tukey or t for Student's t) is shown above the matrix and the standard error of the difference is shown in each cell of the matrix. If you multiply the test statistic by the standard error of the difference, you obtain the minimum significant difference (LSD or HSD).
Thank you very much for posting this solution. I was tired of seeing all the suggestion based on one way ANOVA when the question was clearly about the minimum significance difference for the interaction effects in the model. For Tukey test on multiple comparisons of interaction effect, Minimum significant difference = Q * std err of difference.
