I am dealing with the co-expression modules using WGCNA.
WGCNA is highly recommend for its softhresholding and preservation analysis of the expression data.
The method can automaticly generate some modules (networks) in co-expression manner.
Basically, the co-expression modules can be obtained as followed,
1) calculate the pearson correlation of the expression matrix
2) set a predefined cutoff (e.g., 0.8~0.9) to obtain those highly connected edges
3) apply k-means, SOM... clustering method to obtain the modules,
However, these clustering method required a given number for the expected clusters.
I am wondering if there is any tool that can take the expression matrix as input, and automatically obtain the co-expression modules?