Hello list,

I am a graduate student doing some micorarray experiments on social  
behavior in ants. I've recently started using limma, and have been  
pleasantly surprised by the elegance of its implementation. This is  
my first question to the list.

My experiment is a 3 point time-course that I set up as a loop design  
on our two-color cDNA arrays:
	T0 -> T1 -> T2 ---> (back to T0)
My 10 replicates of this are dye-balanced.

My favorite contrasts are T1-T0 and T2-T0. I can get my genes  
estimated relative expression levels through either topTable or by fit 
$coefficients.
However, I would like to visuallze relative expression levels, at the  
level of individual replicates. That way I can get visual feeling of  
how much variability there is between my replicates. And do  
clustering as if I had used a reference design.
So for each gene I want 10 values for T1-T0, and 10 values for T2-T0.  
I could get these by simply taking the numbers from my direct  
comparisons. But it feels wrong ignoring the information provided  
indirectly about T1-T0 through (T1-T2)+(T2-T0).

How would you go about this?

Thanks for any tips,

Yannick


--------------------------------------------
           yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
    http://www.unil.ch/dee/page28685_fr.html



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