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 __________________________________________________ [[alternative HTML version deleted]]