[galaxy-user] Cuffdiff statistical calculations are inconsistent?
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/
Re: [galaxy-user] Cuffdiff statistical calculations are inconsistent?
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/
Re: [galaxy-user] Cuffdiff statistical calculations are inconsistent?
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/
[galaxy-user] Knowing who is currently logged into your system
Hello All, I was wondering if there is a way to know all the users logged into your local galaxy server? Thanks, -Akshay Choche ___ 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/
[galaxy-user] User dropdown menu as galaxy input file
Good afternoon, I have a query that I hope you can help me with. I am using RGalaxy, and have successfully built a number of useful tools for my instance of Galaxy, using this in R. At the moment, all these tools are using the default galaxy input file, following the example tools. Is there a way I can create an additional input for the tool, that the end user selects, and make this in the form of a drop-down list? So to illustrate with code, I have: inputfile = GalaxyInputFile() #this is the default input file option I would then like an additional input file option, ideally in the form of a drop-down box, that would then be used as an input for a function. What is the best way to do this? Kind regards, Alex Alex Upton, BEng, MRes, PG Cert Business Administration PhD Researcher Biomedical Informatics, Signals and Systems School of Electronic, Electrical and Computer Engineering, College of Engineering and Physical Sciences, University of Birmingham Edgbaston, Birmingham, B15 2TT, United Kingdom Fax: +44 121 4144291 (school general office) Email: a.up...@pgr.bham.ac.uk Personal Web: http://postgrad.eee.bham.ac.uk/uptona/ ___ 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/
Re: [galaxy-user] [devteam-bioc] User dropdown menu as galaxy input file
Hi Alex, On Tue, Mar 12, 2013 at 6:25 PM, Maintainer maintai...@bioconductor.org wrote: Good afternoon, I have a query that I hope you can help me with. I am using RGalaxy, and have successfully built a number of useful tools for my instance of Galaxy, using this in R. At the moment, all these tools are using the default galaxy input file, following the example tools. Is there a way I can create an additional input for the tool, that the end user selects, and make this in the form of a drop-down list? So to illustrate with code, I have: inputfile = GalaxyInputFile() #this is the default input file option I would then like an additional input file option, ideally in the form of a drop-down box, that would then be used as an input for a function. What is the best way to do this? Something like this (from ?galaxy): plotTitle=c(TitleA=A, TitleB=B) Or in the devel version, which has a substantially different API: plotTitle=GalaxyCharacterParam(c(TitleA=A, TitleB=B)) Dan Kind regards, Alex Alex Upton, BEng, MRes, PG Cert Business Administration PhD Researcher Biomedical Informatics, Signals and Systems School of Electronic, Electrical and Computer Engineering, College of Engineering and Physical Sciences, University of Birmingham Edgbaston, Birmingham, B15 2TT, United Kingdom Fax: +44 121 4144291 (school general office) Email: a.up...@pgr.bham.ac.uk Personal Web: http://postgrad.eee.bham.ac.uk/uptona/ devteam-bioc mailing list To unsubscribe from this mailing list send a blank email to devteam-bioc-le...@lists.fhcrc.org You can also unsubscribe or change your personal options at https://lists.fhcrc.org/mailman/listinfo/devteam-bioc ___ 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/