If the user chose the Automatic construction method, module detection uses default values for the needed parameters.
If the user chose the Manual construction method, he/she will have access to the following parameters:
The parameter values will influence the way WGCNA defines the initial set of gene modules. The user can click on the Define Initial Modules button to launch the computation.
The modules can then be iteratively merged (by clicking on the Merge Close Module button) if they are similar enough (i.e. below the merge threshold). The red line in the Clustering of module eigengenes plot shows roughly which modules going to be merged (the grey module is never merge). As the merging works iteratively decreasing the Threshold to Merge Modules between 2 iterations will have no effect.
For the manual computation, the modules are defined initially using the default parameters but their values can be changed and the modules will have to be re-initialiased by clicking on the Define Initial Modules button.