Preparing Files for EEM

Before using EEM, please prepare the following two files:

  1. Expression dataset
    This file includes features (genes or probes), samples, and an expression value for each feature in each sample. The two file formats are available: GCT, Gene Cluster Text file format (*.gct), and TXT, Text file format for expression dataset (*.txt), which are supported in GSEA.
  2. 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 GMT, Gene Matrix Transposed file format (*.gmt).
For descriptions and examples of each file format, please have a look at the GSEA file formats documentation.


Running EEM

1. Uploading Files

1.1 Uploading Local Files

If you have your files on your machine, please choose the 'Local File' option a select your files with the 'Choose File' dialogue. Please make sure, that the individual file size of each file is below 64MB.

1.2 Uploading Remote Files

If your files already reside on a publicly accessible server, you can choose the 'Remote File' options and specify the URLs of your files.

1.3 Using Example Files

If you want to used built-in examples files, please select the 'Example' option.



2. Starting the supercomputer

After everything is checked, we are ready to start EEM on the supercomputer.


3. Registering email for notification

If you want to receive messages about the completion or your EEM calculations, please register your email. Alternatively you can bookmark the site and come back to it later. However, after 14 days your data will be deleted and the site with your results will no longer be available.



5. View and download your results

After the calculations are finished, the results can be viewed online or download in a non-server-depended format. The downloaded results can be view locally with a web browser. For visualizing and presenting the results as a webpage, the Nozzle R Package is used.