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
Hi Jen,
Thank you for your answer.
However, the output file transcript differential expression testing gives the
ratio (log2 of the fold change) of FPKM of a specific transcript between two
conditions, which means this fold change in FPKM does not take the overall gene
expression into
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
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