Hi there,
Looking at the output of the SplicingDiff files of CuffDiff, me and my
colleagues are preplexed about the output of the p_values and q_values.
We've tried different inputs of different samples to compare but never seem
to manage to get p_values smaller than 0.50 and we keep getting
Felix,
You seem to be providing the correct inputs to Cuffdiff and it appears to be
producing valid output. More information about setting parameter values and
interpreting Cuffdiff can be found in manual:
http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
Good luck,
J.
On Jun 16, 2011, at
What version of Cufflinks is your Galaxy installation running? A recent version
(1.00 and 1.01) had a problem that was causing the splicing and promoter use
tests to have very few differentially regulated genes, according to
http://cufflinks.cbcb.umd.edu/.
-rory
On Jun 16, 2011, at 8:13 AM,
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