Repeated measures with correlated measures (not time) Most repeated measures ANOVAs have time as the repeated measure; I was wondering about using a repeated measure that is not time.
Say we fed two groups of animals different diets. At the end of the experiment, we sample the tissues, and measure ~30 different compounds (e.g. different fatty acids [FA]).  Animals are sampled but once. Each FA is not independent of each other, as some of these compounds are converted from one form to another. As such, they are frequently moderately correlated with each other.
Would it be fair to treat each compound as a repeated measure, with diet as a between subjects factor? Thus, the interaction between Diet X FA would tell me if the FA content differed among diets?
I note that in many papers, researchers would perform 25-30 separate ANOVAs; one on each compound. Yet, these compounds are not independent of each other, as they are each measured simultaneously on the same animals.
Thanks for any pointers.
 A: Have a look in a Multivariate text for MANOVA--multivariate ANOVA.  Here is a website...
http://faculty.chass.ncsu.edu/garson/PA765/manova.htm
Though, that's a lot of dependent variables and it could be hard to interpret.  It might be simpler to do some sort of data reduction first, like PCA among your set of fatty acids.  I suppose it depends on how much overlap there is and how many PCs you'd need to extract to account for the 30 vars.
A: It's interesting... how do you compare the compounds with each other?  Repeated measures don't have to be necessarily over time, but they need to be measures of the same thing or things that can be treated as if they are the same.  You could certainly measure the same compound in different areas of the body and that would be a repeated measure.  
I guess I'm asking the first question out of ignorance of your field.  If you can compare the compounds one to another then they are repeated measures grouped by individual animal.
I suppose one could even consider multi-level modelling beyond simple repeated measures because you could take the comparable body part as one level and the animal itself as another.
