Running GSEA or comparable analysis with multiple variable interaction?
I'm not sure I understand &quot;I would like to run GSEA or a similar analysis to find WGCNCA clusters that differ based on the interaction between the two main variables&quot;. I would run an association analysis (regression) for module eigengenes and the appropriate interaction term. The (most) significant modules are your candidates. This step is simply regression (in the simplest case a linear model should be sufficient), no GSEA needed. You can then subject the identified modules to GSEA or similar to get an idea of their biological function.