Preparing Files for EEM
Before using EEM, please prepare the following two files:
Expression datasetThis 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.
Gene setsThis 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).
1. Uploading Files
1.1 Uploading Local FilesIf 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 FilesIf 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 FilesIf you want to used built-in examples files, please select the 'Example' option.
2. Starting the supercomputerAfter everything is checked, we are ready to start EEM on the supercomputer.
3. Registering email for notificationIf 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.