Hello Jianguang,

Fold is included in the Cuffdiff output. Section "Differential expression tests", first file, column #9.
http://cufflinks.cbcb.umd.edu/manual.html

Hopefully this helps,

Jen
Galaxy team

On 9/4/12 1:16 PM, Du, Jianguang wrote:
Dear All,

I am looking for the differential splicing events between cell types.
However the Cuffdiff gives output using "the square root of
Jensen-shannon divergence" to measure the difference.

Although I tried my best to understand "the definition of the square
root of Jensen-shannon divergence", I still could not understand the
meaning of a specific value of "the square root of Jensen-shannon
divergence". I would appreciate it very much if anyone let me know how
to covert "the square root of Jensen-shannon divergence" into "fold".
For example, how much "the square root of Jensen-shannon divergence" is
"2 fold difference" equal to.

Thanks in advance.

Jianguang



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