I am trying to use gage package to do gene set enrichment analysis and I am able to get a result from the main gage function but now want to make a scatterplot and heatmap of the results. The issue I am having is how to correctly define the setp argument using the results of the main function which includes both greater than and less than. Can someone give me a clue on how to create proper input from the results. I can include a snapshot or code from my script.
Peter Chernek, MPH