Run differential expression to create a comparison for GSEA
When running gene set enrichment analysis (GSEA) in Pluto, you're prompted to select a comparison. The dropdown list is populated with differential expression analyses that you've previously run for the experiment.
If you don't see the comparison that you're looking for in the dropdown list, you'll first need to create a new differential expression analysis.
Once the differential expression analysis has finished running, the comparison will appear in the dropdown list for GSEA.