I am sure this has come up before and maybe I missed the answer.
If in using cuffdiff I run a sample 1(3 repeats) vs a sample 2 and then run the same sample 1(3 repeats) against a sample 3 or a sample 4, I get different value for fpkm from sample 1 each time.
Is there something going wrong here or is there something in the program that causes this difference?