Hi vijay I'm guessing that what you really want to know, is which genes have a different response to treatement (ie the change in strain A after treatment with P is different to the change in strain B after treatment with P). If so I think design 1 is preferable, set up as a 2x2 factorial model which you can easily setup and analyse with Limma. Design 2 is really just design 1 with no AP-BP, and I don't think will estimate what you want as well as design 1. Design 1 allows you to optimally estimate: the (baseline) difference between strain A and B (alpha=BS-AS), the difference between Peptide and Saline in stain A (beta=AP-AS), which genes have different response to treatement (this is interaction of alpha beta=(BP-BS) - (AP-AS)). Its probably worth having a look at the following paper to understand how different designs perform: Glonek GF, Solomon PJ. Factorial and time course designs for cDNA microarray experiments.Biostatistics. 2004 Jan;5(1):89-111. PMID: 14744830 (or go to our website for a preprint) Also check out the excellent limma users guide. Cheers Chris > > 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 > Dr Chris Wilkinson Senior Research Officer (Bioinformatics) | ARC Research Associate Child Health Research Institute (CHRI) | Microarray Analysis Group 7th floor, Clarence Rieger Building | Room 121 Women's and Children's Hospital | School of Applied Mathematics 72 King William Rd, North Adelaide, 5006 | The University of Adelaide, 5005 Math's Office (Room 121) Ph: 8303 3714 CHRI Office (CR2 52A) Ph: 8161 6363 Christopher.Wilkinson@adelaide.edu.au http://mag.maths.adelaide.edu.au/crwilkinson.html