EDGE includes newly developed methods that allow one to identify differentially expressed genes from time course microarray experiments...
Besides the typical experiments that aim to identify differentially expressed genes across two or more biological conditions, EDGE also allows one to perform significance analysis on time course experiments (Storey et al. 2005, PNAS). Two types of time course significance analyses are possible. One type allows the user to test for genes whose expression changes over time. The other allows the user to identify genes who show different expression over time between two or more biological conditions. Even though some significance analysis packages allow for users to enter information about time points, we have a rigorously developed set of methodology that was recently published. There are many things that can go wrong when applying methods originally developed for traditional "static" analyses to time course experiments, so it is important to use a method that has been explained and justified for this setting.