My experiment involves 12 hybridizations of 3 stages (E, F ,G) and 2 types (Active, Inactive).  The direct comparisons are active (A) to inactive (I) for each stage using 4 biological replicates for each comparison with balanced dye swaps.

I want to see the results of active vs inactive for each stage and then compare the results between stages E -> F and F -> G.  Is this design correct?  Slides 1->4 are stage E, 5->8 are stage F, and 9-12 are stage G.  The first two slides are labelled the same and the last two are dye swapped.  

Slide E_AI F_AI G_AI E_F F_G
1     1    0    0    1   0   
2     1    0    0    1   0   
3    -1    0    0   -1   0  
4    -1    0    0   -1   0  
5     0    1    0   -1   1   
6     0    1    0   -1   1   
7     0   -1    0    1  -1   
8     0   -1    0    1  -1   
9     0    0    1    0  -1  
10    0    0    1    0  -1  
11    0    0   -1    0   1  
12    0    0   -1    0   1   


Or is a contrast matrix the correct method for the indirect comparisons (between stages)?

Thanks.
	[[alternative HTML version deleted]]

