[BioC] experiment-design-advice-request

[vijayaraj nagarajan]

hi friends
we are designing a microarray experiment, where there are two different mouse strains (A,B)...
and one condition (Peptide - P and Saline - S). we expect the mouse strains to express differentially even under normal  (saline) conditions...so we did not want to go for pooling the controls, to have a common - pooled control... under this scenario...
 
which of the following designs would you suggest....(we have planned to use dyeswap and 2 replicates for each hybrisation)....
 
1:
 
AP---BP
|  \  /   |
|  /  \   |
AS---BS
 
(all pairs - with 6 hybridisations)
      OR
 
2: 
 
AP
|
AS---BS
         |
       BP
 
(with just 3 hybridisations, so that we could deduce AP-BP,using AP-AS-BS and rest like that...)
 
i request your valuable advice in this regard....
thanks 
 
vijay
graduate student
department of biological sciences
University of Southern Mississippi
MS
 

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