The confidence intervals provided by Cufflinks/Cuffdiff are a good place to start; any confidence interval that includes 0 should be looked on skeptically.

Good luck, J.

On Jul 3, 2013, at 2:52 PM, Hoang, Thanh wrote:

Hi all, I have been working on RNA-seq data analysis using TopHat and Cuffdiff. One of the problem I have is to define the cutoff RPKM value to tell whether a gene is expressed from the background noise?. Could anybody give me a suggestion? Thank you Thanh ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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