Compute Network

The Network can be constructed either in an automated or manual way (Automatic or Manual Construction Method respectively).

If the user chooses to use the Manual network computation, he/she will have access to parameters for modules detection.

The user can specify the soft power (by default the red value in the previous step) and the Topology Overlap Matrix (TOM) type (only for unsigned network). The central idea of TOM is to take into account the direct connection strengths as well as connection strengths mediated by shared neighbours.

TOM type can be:

Once the parameters are chosen the user can click on the Calculate Network button to compute the network accordingly.

Resulting modules are then represented by their module eigengenes (virtual genes representing each module). The tree of the module eigengenes (Clustering of module eigengenes) is found in the first part of the figure under the parameter box. It represents how correlated the module eigenes are. The second part of the figure (Cluster dendrogram) represents the dendrogram of the genes, the first band of colors represents the initial modules, and the second band represents the merged modules if any.