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Old 04-02-2010, 07:42 PM   #11
RockChalkJayhawk
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Location: Rochester, MN

Join Date: Mar 2009
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The point with RPKM that I do not like, it is that I do not feel that it can handle different coverages.
I totally agree with you Chema. RPKM is biased for testing differential expression for longer genes. See the following paper:

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http://www.biology-direct.com/content/4/1/14
and also other papers by Oshlack and Wakefield.
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