hi, i have the following dataset: - 26 indivuals with expressiondata (log-ratio from common ref design) (random factor: patient) - each individual has expression data from 1 to 3 different (but fixed) locations (fixed factor: location) - 14 controls, 12 patients (fixed factor: group) i am mainly interested in the group effect! i tried limma, but it did not seem to work with my random factor patient?. any suggestions? thanks for help! tina -- Bettina Kulle Andreassen Associate Professor University of Oslo Faculty Division Ahus Institute for clinical epidemiology and molecular biology (Epi-Gen) Sykehusveien 27 N-1474 Nordbyhagen tel: +47 67927762 fax: +47 67927803