
Dear Listers,

 

We have a case-control study and would like to use Agilent 4x44K array.  We only have three biological replicates.  My questions are

 

1.  Do we need to use technical dye-swap or we can use biological dye-swap (budget issue)?  

 

2.  How does the un-balanced dye-swap effect the analysis?

 

3.  If we use biological dye-swap and balanced dye-swap, since we only have three samples for each condition.  Can we pool samples in order to balance dye-swap?  Here is the design:

 

               Array1                      Array2                      Array3                   Array4

Red          caseA                       controlB                    caseC                   pooled control

Green       controlA                     caseB                      controlC                pooled case

 

Many thanks,

 

Jason

 
 		 	   		  
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