Hi all, I would like to know the possible designs that can be defined in a microarray experiment. I know for example one can compare two experimental factors such as treatment and tissue and so the experimental design includes all the possible comparisons between classes of this factors. Other alternative would be to have a reference sample and so the design would only have the comparisons of the rest of samples with it. I would like to know what any other microarray experiment produce what experimental design. For example, a cluster analysis uses any other design apart from this two? A time-course experiment? Is there any other possible analysis that uses a different experimental design? Thanks in advance. [[alternative HTML version deleted]]