unbalanced mixed design

[Andrew Smart]

Apropos Margriets question about a mixed design and permutation test, I tried your suggestion, 
but for a 2 x 2 unbalanced mixed design with the depsamplesF test because I have different 
numbers of subjects in a clinical and control group, and two conditions. I tried a design matrix 
with row 1 for condition ("1" and "2")
row 2 subject number and  the third row group (1 and 2). 

So the design matrix is 3 X 22 like this:
condition:       1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2
subj number: 1 2 3 4 5 6 7 8 9 10 11 1 2 3 4 5 6 7 8 9 10 11
group:              1 1 1 1 1 2 2 2 2 2 2 1 1 1 1 1 2 2 2 2 2 2 

However, the resampledesign function wants the design matrix to be constant within a block and 
since I have an unbalanced design this doesn't seem to be possible.

Is there work around to set up the design matrix with an unbalanced design to call the F statistic 
for the permutations? I do not want to throw away a subject to make the design balanced because 
I have already so few subjects in this experiment. 

Thank you,
Andy

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