EEM needs two types of inputs: an expression dataset of interest and a gene set library that includes gene sets used as seeds of modules. EEM assumes coherence as an indication of the functionality of gene sets; i.e., if a gene set have some function, the member of the gene set should be coherently expressed in the expression dataset. Under this assumption, EEM screens a gene set library for gene sets that have a signifcantly large coherent subset in the expression data set. From the gene sets that passed the screening, EEM extracts coherent subsets as expression modules.

Session ID xGPZx
Expression Dataset
Advanced Preprocessing Options...
Preprocess the expression file. Convert probe IDs to gene symbols.
The CHIP file format contains annotation information about a microarray. It lists the features (i.e probe sets) used in the microarray along with their mapping to gene symbols (when available).
More information about the CHIP file format can be found here.
Convert Expression Value to the log-scale.
Number of genes after variation filter (default=8000)
This file includes features (genes or probes), samples, and an expression value for each feature in each sample. The two file formats are available: A simple tab-delimited format for expression dataset (*.tab, example), or the GCT Text file format (*.gct), which are supported in GSEA.
Gene Sets
This file includes one or more predefined gene sets like gene sets from the Molecular Signature Database (MSigDB) or your own defined gene sets. For each gene set, the gene set name, its brief description, and genes in the gene set are given. The file format should be followed by the GMT file format (*.gmt, example).