I am running an experiment to determine if a treatment delivered to a subject changes a measured outcome variable (y). The experiment on the subject was divided in to phases: Phase 1 was the control, Phase 2 and 3 had treatment delivered, and Phase 4 and 5 were washout phases. The outcome variable was measured over all phases. Now, I am doing an ANOVA matched pairs test (using Fit Y by X in JMP8.0) using the subject ID as the "matching column" to determine if phase has an effect on y. I would now like to compare the y means in the different phases.

My question is does the "Compare Means" command under the one way ANOVA take in to account the matching column? I suspect that this is not the case because even though Phase has significant effect on y (in the matching fit), none of the comparison circles shows a significant difference. Any suggestions on how I might do this comparison would be helpful.

Thanks in advance.