It allows to build a more complete object and generate richer reports about the expression data. Sample annotation can be supplied in a data.frame that specifies a class for each sample. Classes can represent different conditions, phenotypes, cell lines, time points, etc.

CEMiTool can determine which biological functions are associated with the modules by performing an over representation analysis (ORA). To do this you must provide a pathway list in the form of GMT file. CEMiTool will then analyze how these pathways are represented in the modules.

Interaction data, such as protein-protein interactions can be added in order to generate annotated module graphs. Interaction files contains two columns for interacting pairs of genes

The beta value is a parameter that lies in the core of the weighted gene co-expression network analysis (WGCNA).