To run GSEA, first select the differential comparison you'd like to use as input
When running pathway analyses such as Gene Set Enrichment Analysis (GSEA), you first need to set up a differential comparison by running differential expression analysis. Depending on your experimental design, you may have one or more differential comparisons that you've run. For example, in the experiment below, the are two comparisons:
1. Low ethanol vs no ethanol treatment
2. High ethanol vs no ethanol treatment
When you create a new GSEA analysis in Pluto, you're prompted to select a comparison to use as input for the pathway analysis. The dropdown list is populated with those differential comparisons that you've previously run for that 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.
Otherwise, select the differential comparison that you would like to perform pathway analysis on. Remember: you can always go back and run additional GSEA analyses for all comparisons in your experiment.
