Cells were added to all wells in what should be equal numbers, but because of potential imprecision, pre-treatment activity was measured (activity is proportional to cell count). Activity was measured again post-treatment.

I was advised to perform an ANCOVA on my data (3 IVs, post-treatment measurement as the DV, and pre-treatment measurement as the covariate). Pre-treatment activity was a significant covariate and a three-way interaction between the IVs was identified (as expected). Now I'm stuck. A few questions:

- I learned that a 3-way interaction in an ANOVA requires 2-way ANOVAs for each of the levels of the third IV to tease out main effects, but what do I do with a 3-way ANCOVA interaction? Part of my dilemma: I want to report the "adjusted" post-treatment measurements as if all groups had started off equivalently, but the adjusted means are different for the 3-way ANCOVA vs. the 2-way ANCOVAs, since a subset of the data is used in 2-way ANCOVAs. Which adjusted means are the proper ones to report, and in general how is a 3-way ANCOVA interaction decomposed?

- How do I handle my "gold standard?" Is it appropriate to include it in the ANCOVA (so that its mean also gets adjusted), or does that invalidate the analysis? I don't want the focal point to be comparing every other cocktail to the standard; I only want the standard included as a point of reference.

- Three post-treatment measurements were taken to observe early-, mid-, and late-onset effects. In terms of a timecourse, is it appropriate to simply run an ANCOVA for each time point and observe the introduction/disappearance of significant effects?

This is a lot, so any help is appreciated!