Hi, I would like to compare 2 RNA sources to see if a culture medium mimetic the plant host. There are evidence that a culture medium mimetic the plant, then I inoculated the phytopatogenic bacteria in both, mimetic culture medium and plant. After 24 hours, I was collected the RNA and did a 3 hibridizations: Cy3 Cy5 mimetic culture medium vs NA mimetic culture medium vs NA mimetic culture medium vs NA Cy3 Cy5 plant vs NA plant vs NA plant vs NA NA = poor culture medium I have hybridized they separated because I will use it in a time course experiment. I thinking to do a contrast like limma usersguide (11.5 Weaver Mutant Data: A 2x2 Factorial Experiment). If the mimetic medium is true (mimetic the plant) I don't will get any differentially expressed genes. This aproach is good or you suggest me other? Thank you very much -- Marcelo Luiz de Laia Ph.D Candidate S?o Paulo State University (http://www.unesp.br/eng/) School of Agricultural and Veterinary Sciences Department of Technology Via de Acesso Prof. Paulo Donato Castellane s/n 14884-900 Jaboticabal - SP - Brazil Phone: +55-016-3209-2675 Cell: +55-016-97098526