I have a question about raw read counts and rpkm. After I get gene counts and fpkm from cufflinks, I found some housekeeping genes (ACTB, GAPDH, RPLP0, UBC) have the similar expression trends in counts and rpkm.
I don't understand why. Does that mean the normalization in rpkm have no affections to housekeeping genes?
Thanks a lot! Cam