GSEA analysis - example dataset/dataformat


I have seen that there is a GSEA button after “Genes/protein list(s) upload” but it has always been unabled to use even though with all the example datasets available. So I wonder if there will be an example dataset available anytime soon or an explanation of how to format the input data, preferably by uploading a csv? In addition, is it possible to upload a metadata file together with an assaydata file?
Thank you for your help!


Hello Timo,

GSEA is typically designed to work with gene expression datasets rather than lists of genes or proteins. The current assumption for list upload is that gene/proteins uploaded are significant genes identified after DE analysis. GSEA requires a ranked list of all genes in the study. I suggest you use Single expression table module for GSEA.


This topic was automatically closed after 21 hours. New replies are no longer allowed.