how to perform the GSEA for multi groups

Question

[alwayshope]

Dear experts,

How to perform the GSEA for multiple groups?

Thank you very much for guidance!

Answer 1

[rfran010]

I'll be honest, I don't know what the schematic is showing. But, did you have a chance to view this resource: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

I usually stick to GCT and CLS files. In the GCT you will list all your samples as columns then in the CLS you would group/subgroup them however you like. If you specifically want to run them as two separate groups, then make separate files.

[alwayshope]

This is super helpful. I will try to use the GSEA and make the input using GCT and CLS format instead of using the fgsea R package.

Thank you very much for your kind guidance!