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Old 01-31-2011, 12:58 PM   #1
Location: Montreal

Join Date: Sep 2010
Posts: 19
Default cuffdiff: same run but different FPKM, your thoughts?

I was wondering how cuffdiff would differ if I run it on the same data.
Here are the fpkm of 4 runs for a gene: 38.2168 2.50089 32.3986 39.0589
Same runs about another gene: 46.8446 37.5176 61.7281 33.5432

Do you experience the same phenomenon?

How can we trust these FPKM if it is variating so much?

Thx for your thoughts.
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