I try to do GSEA. Therefore, I downloaded mRNA data files(GCT) from firebrowse. Then i did ranknormalization by using Gene pattern. After that, i opened GCT files by using EXCEL and figure out that tumor and normal tissue RNA data are mixing in. So can i exclude the normal tissue data ?? Then do GSEA?? or Include the tumor and normal tissue RNA data. Then do GSEA??
Thank for reading my question Pleas give comments please.