The main EDGE window. The various tasks that can be performed are shown on the menu. The user simply selects one of them and presses GO
The window used to identify differentially expressed genes. The classes across which differential expression is to be discovered can be designated, along with information about the experimental design and the number of null iterations.
The differential expression results window. Once EDGE has finished performing the significance calculations for differentially expressed genes, it is possible to adjust the significance cut-off according to either q-values or p-values. It is also possible to observe the global behavior of these in order to choose a sensible cut-off that balances false discoveries to the number of significant genes. A singificant gene can be selected and its information looked up at NCBI according to its gene name (e.g., an accession number or UID). A hierarchical clustering of the signficant genes can be constructed.
An example plot in EDGE. Various plots can be made in EDGE, including eigen-genes, boxplots, and hierarchical clusterings (as shown below).