Forgive me if this question has been answered before, but my searching on this site did not provide the precise answer that I need.
I have RNA-seq data for 2 conditions, A and B. I have the unique gene IDs, and their corresponding reads, which I converted to TPMs. Then, I calculated the p-value for these 2 conditions for all the genes. Now since I have the expression levels also, I created a volcano plot which basically gave me the list of genes that have a significant p-value for these conditions (<0.05) AND for which the fold-change is 2 times or higher for condition B as compared to condition A. So now I have a list of ~200 genes with their corresponding p-values.
Now, I need to perform GSEA on this list of genes, to see if this list of genes is enriched in any biological pathway etc. So, I wanted to know how I can do that. I have installed the GSEA software to my Ubuntu system, and I think (based on what I understood from the GSEA user guide) I need to choose the GSEA mode where I provide my own gene set, but I am not very sure.
Any help would be great!