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Old 01-21-2014, 03:02 PM   #4
Zapages
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Location: NJ

Join Date: Oct 2012
Posts: 94
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I read it on seqanswers: http://seqanswers.com/forums/showthread.php?t=39758

I was experiencing the same issues as you were by looking through the expression results from Cufflinks and was very concerned as to why confidence values were off.

Also when you continue on to Cuffmerge and Cuffdiff. Please use the same version ie.if you used 2.0.2 for Cufflinks then use 2.0.2 version for Cuffmerge and Cuffdiff. Likewise for Cufflink/Cuffmerge/Cuffdiff 2.1.1.

All the best with your project.
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