Design 1 is better than 2 but is unbalanced for the dye effect. If there could be a dye by gene interaction you may have some difficulties in interpreting the design. Design 2 is unbalanced for the main effects. You would be better to complete the loop, with 4 hybridizations. I am not sure what you mean by "dyeswap and 2 replicates". Are you using 6 or 3 arrays, or is this the base design which you intend to replicate? If you plan to have 8 or 12 arrays, you have many more choices for the design. Finally, technical replication is not that informative. If at all possible, each hybridization should be done with an independent biological sample. Technical replication is done mainly if the cost of creating an independent biological sample is too high. (Technical replication is also done due to the misconception that it is necessary for dye-swapping.) Just a note - statisticians consider the control to be a condition, so you actually have 2 conditions. --Naomi At 02:49 PM 4/30/2005, you wrote: >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]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111 [[alternative HTML version deleted]]

hi anja, christopher and naomi thanks a lot for those nice suggestions. i read that paper by Glonek and Solomon. that was really helpful. thanks again vijay Anja Schiel <a.e.schiel@lumc.nl> wrote: Hi Vijay I recommend reading an article from Glonek and Solomon (Biostatistics, 2004, 5,1,89:111). You will find good arguments for the loop design and why certain comparisons are not as informative as others. Anyhow, there are a lot of good articles about microarray design available. Anja On Sat, 2005-04-30 at 11:49 -0700, vijayaraj nagarajan wrote: > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Anja E. Schiel, Ph.D. Departments of General Internal Medicine and Human Genetics Leiden University Medical Center PO Box 9503 2300 RA Leiden The Netherlands tel: -31-(0)71-5276067 fax: -31-(0)71-5276075 __________________________________________________ [[alternative HTML version deleted]]