I'll preface my concern by saying that I'm a novice to Cufflinks.  Back in
September, I performed a Cuffdiff analysis comparing a wild-type and mutant
condition.  The analysis returned ~800 transcripts differentially regulated
between the two with statistical significance.  Recently, I've rerun the
Cuffdiff analysis - using exactly the same files stored in Galaxy for all
inputs, and with all the same parameters - and only get a few dozen
statistically significant hits.  However, all of the data besides the p and
q values are essentially identical between these two runs, so I am really
unclear as to what is causing the difference.  Here is just one clear

>From run 1:
FPKM 1 = 17.2434
FPKM 2 = 196.735
log2(fold change) = 3.51214
p = 1.64E-8
q = 7.33E-6
significant = yes

>From run 2:
FPKM 1 = 14.4489
FPKM 2 = 144.939
log2(fold change) = 3.32641
p = 0.000170034
q = 0.0719964
significant = no

The second Cuffdiff analysis shows there is still a ~10-fold difference
between conditions, but this is not statistically significant.  Has the
version of Cuffdiff on Galaxy been updated such that some parameters have
changed, that could explain this difference?  Or, is there some setting I
am missing that would cause very large changes to fail statistical
significance testing?  Any help or input would be appreciated, I am really
at a loss for why executing what should be exactly the same task is giving
vastly different results.  I could just be overlooking something very
fundamental that is obvious to someone with more experience with this
program.  Thanks.

-Jenna Smith
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