This is likely due to the upgrade from Cufflinks 1.3.x to Cufflinks 2.0.x; Cufflinks 2.0 introduced a new algorithm for Cuffdiff in particular. You can read about these changes on the website: http://cufflinks.cbcb.umd.edu/ (and there's a manuscript describing the changes as well).
You might consider writer to to the tool authors directly for more details: tophat.cuffli...@gmail.com Of course, please consider sharing anything you learn with members of this list as well. Best, J. On Mar 13, 2013, at 12:06 PM, Mohammad Heydarian wrote: > We are having the exact same issue, on the main server and our (recent) cloud > instances. > > Were some of the hidden Cuffdiff parameters modified since fall 2012? > > Cheers, > Mo Heydarian > > On Mar 13, 2013 11:02 AM, "Jenna Smith" <jes...@case.edu> wrote: > Hi, > > 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 example: > > From run 1: > YFR026C > 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: > YFR026C > 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 > > > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/
___________________________________________________________ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
