Dear R-Users, I use home-made spotted arrays to do some research contected with alergies. The matrix consist of : 60% of the genes are up-regulated and 40% of genes that are down-regulated and spikes. I didn't use any genes with constant expression. How I should analyse this experiment? According to statistics I should focuse on external spike controls and compare all genes with spikes. It is two coulour experiment. So I have to build quite complicated statistical model. I'm not sure if it is a right pathway. What do you think? Regards, Barbara