I am faced with a dilemma, I have run and obtained output from Cuffdiff and was looking to input it into GSEA and CummeRbund, but my gene Ids are Xloc for some reason. For GSEA in particular, I can't run the genes.fpkm_tracking file with the software because there is no available reference built in that accepts Xloc. Would there be a way to convert these IDs to Ensembl (ENST) or to create a .chip file for GSEA that allows the Xloc IDs to be read in? What is the common rule of thumb for this issue?
Any help on this matter would be greatly appreciated!