Hi all, I need some help in designing a microarray experiment. We want to analyze the effect of a treatment on gene expression of three genotypes of Arabidopsis and we would like to answer to two questions: 1) what are the differences between genotype transcriptomes 2) what is the effect of the treatment on each genotype: what genes respond differently to the treatment between two genotypes ? We thus have a factorial design with two factors: treatment (untreated, treated) and genotype (wild type, mutantsr) for which we want to test the main effects and the interaction In addition we planned to do three independent biological experiments (to be considered as a block factor ?). We will use two-color microarrays with dye-swap. Thus my question is what is the best design to use for hybridization ? Should I use a common reference (for instance untreated wild type) for all arrays of the same biological experiment or for the three experiments ? Or is there a better design for answering the above questions ? Thank you for your help -- Christian Brière "Cytosolic and nuclear calcium signalling" group UMR CNRS/UPS 5546 BP42617 Auzeville F-31326 Castanet-Tolosan (France) Tel: +33(0)5 34 32 38 90 Fax: +33(0)5 34 32 38 02 http://www.lrsv.ups-tlse.fr [[alternative HTML version deleted]]