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Old 10-12-2011, 04:41 AM   #1
Location: Tokyo, Japan

Join Date: May 2010
Posts: 27
Default RPKM and expression comparison

When you use RPKM for expression value and want to compare the value of multiple genes, what are the things you should be careful with?

Theoretically, RPKM is normalized expression value which used by the length of transcripts and the amount of reads per sample, so it looks OK for me to use this value for expression comparison between the genes with long transcript and the genes with short transcript.
But could be the nature is not so simple.

If you know some information regarding RPKM and expression comparison, please tell me.

kenosaki is offline   Reply With Quote
Old 10-19-2011, 02:39 PM   #2
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Location: Stanford

Join Date: Jun 2009
Posts: 181

FPKM doesn't behave nicely and basically isn't directly suitable for statistical comparisons. Cuffdiff has a sophisticated solution:
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