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.
You only include one gene set in your analysis, hence there is only 1 row in the result matrices.
sigGeneSet assumes that you have multiple gene sets, and tries to select the significant ones (rows) from the result matrices. That’s why it threw error.
In your case, you don’t really need to use sigGeneSet. Your gene set was very significant based on the p.val and q.val columns (both 0’s) from results$greater (test for up-regulation).
Ok thank you Weijun! So what would be the best way to make a scatterplot or map to visualize the results$greater to show how the set is up-regulated among the entire mRNA expression matrix? How would you interpret the greater than result? Would you say the set is significantly upregulated in comparison to the exprs=y?