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?

I have seen this with online Galaxy and with the instance I have on my Mac

el linney
Duke University
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