[R] contrast matrix for aov

[Darren Weber]

Prof Brian Ripley wrote:

> On Wed, 9 Mar 2005, Darren Weber wrote:
>
>> How do we specify a contrast interaction matrix for an ANOVA model?
>>
>> We have a two-factor, repeated measures design, with
>
>
> Where does `repeated measures' come into this?  You appear to have 
> repeated a 2x2 experiment in each of 8 blocks (subjects).  Such a 
> design is usually analysed with fixed effects.  (Perhaps you averaged 
> over repeats in the first few lines of your code?)


Each subject experiences multiple instances of a visual stimulus that 
cues them to orient their attention to the left or right visual field.  
For each instance, we acquire brain activity measures from the left and 
right hemisphere (to put it simply).  For each condition in this 2x2 
design, we actually have about 400 instances for each cell for each 
subject.  These are averaged in several ways, so we obtain a single 
scalar value for each subject in the final analysis.  So, at this point, 
it does not appear to be a repeated measures analysis.  Perhaps another 
way to put it - each subject experiences every cell of the design, so we 
have "within-subjects" factors rather than "between-subjects" factors.  
That is, each subject experiences all experimental conditions, we do not 
separate and randomly allocate subjects to only one cell or another of 
the experiment.

I hope this clarifies the first question.  I will try to digest further 
points in this thread, if they are not too confounded by this first 
point of contention already.