Hi, I have some microarrays to do analysis. It includes 2 factors: 1week old and 5week old as ageing factors (two level) , and 4_levels genotype (yw, GMH5xyw, GMH5xFOXO,GMH5x4EBP) I assume the matrix is 1week 5week yw b0 b0+b(Ageing) GMH5xyw b0+b(Genetic) b0+b(Ageing)+b(Genetic) GMH5xFOXO b0+b(Genetic)+b(FOXO) b0+b(Genetic)+b(FOXO)+b(Ageing) GMH5x4EBP b0+b(Genetic)+b(4EBP) b0+b(Genetic)+b(4EBP)+b(Ageing) is it reasonable to do this analysis to extract effects of b(Genetic),b(Ageing),b(FOXO),b(4EBP) using limma and how to write matrix in code? thanks Zhi Zhang, Ph. D. Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Rd. La Jolla, CA 92037, USA Zhi Zhang, Ph. D. Sanford-Burnham Medical Research Institute Building 7, Bodmer lab 10901 North Torrey Pines Rd. La Jolla, CA 92037, USA Phone 858-646-3100 ext. 3801 Fax 858-795-5298 [[alternative HTML version deleted]]