Hi, All,

I have a very specific experiment design trying to compare two  
samples as follows:



cy3	cy5
1		Reference		A
2		Reference		A
3		Reference		A
4		B		Reference
5		B		Reference
6		B		Reference
There're a total of 6 arrays, and they all used the same common  
reference; but unfortunately the 2 experimental samples are labeled  
with different dye. I'm using limma trying to get differentially  
expressed genes between A and B. There're clearly a dye effect here.  
Since there's no dye swamp within each sample, it make it hard to  
estimate the dye effect using limma. But they share a common  
reference labeled with 2 different dye. I 'm wondering if there's any  
way to use this information to estimate dye effect.

Any help would be greatly appreciated!

yan




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