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Old 07-21-2011, 03:24 AM   #1
fabrice
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Location: paris

Join Date: Oct 2009
Posts: 86
Default RNA-seq pair-end normalization between samples, FPKM from cufflinks 1.0.3

Dear expert,

I have runed cufflinks 1.0.3 to get the FPKM value for each Illumnina RNA-seq pair-end sample.

When run cufflinks, I do not set these parameters:
--upper-quartile-norm
--total-hits-norm
--compatible-hits-norm

Now I want to do normalization between samples, does anyone have some suggestions? Using DEseq? or Limma?

Thank you very much in advance.
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