Hi all, ok if execution time will remain reasonable, I'll not change the B setting too like my first run; otherwise, at least for the current possibilities of sharing and co- working server, I'll set it below about 100 also because I think a p-value of 0.01 is already quite stringent and restrictive on my dataset. Best, Giovanni Laboratory of Preclinical and Translational Research IRCCS - CROB Oncology Referral Center of Basilicata Rionero in Vulture - Basilicata - Italy 2014-02-24 15:54 GMT+01:00 Kasper Daniel Hansen <khansen@jhsph.edu>: > Do note that these p-values are corrected for multiple testing because of > the way they are computed. So 0.001 is not so bad. > > Kasper > > > On Mon, Feb 24, 2014 at 9:37 AM, James W. MacDonald <jmacdon@uw.edu>wrote: > >> Hi Giovanni, >> >> Tim advised you to do the exact opposite. If you set B = 100, then the >> smallest p-value you can achieve is 0.01, which as he says, 'sucks'. If you >> use B = 1000, the smallest p-value will be 0.001 which is marginally better. >> >> Best, >> >> Jim >> >> >> >> On 2/24/2014 5:46 AM, Giovanni Calice wrote: >> >>> Hi Tim, >>> I'm already in the order of ideas to set the n of resamples below about >>> 100 as you say. >>> I await news about your comments for a better marginal test statistic and >>> the reference discussion about this topic. >>> >>> For now I'll follow your advice and previous ones. >>> >>> Thank you very much. >>> >>> Best, >>> Giovanni >>> >>> >>> Laboratory of Preclinical and Translational Research >>> IRCCS - CROB Oncology Referral Center of Basilicata >>> Rionero in Vulture - Basilicata - Italy >>> >>> >>> 2014-02-23 5:47 GMT+01:00 Tim Triche, Jr. <tim.triche@gmail.com <mailto:="">>> tim.triche@gmail.com>>: >>> >>> >>> Don't do that. B is the number of permutations. Your >>> significance estimates will suck if you set it below about 100. >>> If you can wait (a day or so) for 1000 or more permutations, they >>> will be quite good. I have some ideas for a better marginal test >>> statistic to capture the omnibus null of "no difference" against >>> any reasonable alternative, but that's a topic for another >>> discussion. It won't change the fact that you need a lot of >>> permutations to get solid significance estimates from a biased >>> sample (450k chip). >>> >>> Best, >>> >>> >>> Statistics is the grammar of science. >>> Karl Pearson <http: en.wikipedia.org="" wiki="" the_grammar_of_science=""> >>> >>> >>> On Sat, Feb 22, 2014 at 10:02 AM, Giovanni Calice >>> <giovcalice@gmail.com <mailto:giovcalice@gmail.com="">> wrote: >>> >>> Hi, >>> >>> I missed to ask advice about B parameter. >>> In my first bumphunter runs, I set B=1 (default setting) >>> having thus >>> results within a reasonable time. >>> >>> Now, as mentioned in the previous mail, I set B=1000 according >>> to the reference >>> manual and >>> I thought so in order to have a statistically significant >>> results. >>> >>> In my next bumphunter call, have I to change this setting >>> (B=1000)? >>> >>> Thanks, >>> Giovanni >>> >>> >>> Laboratory of Preclinical and Translational Research >>> IRCCS - CROB Oncology Referral Center of Basilicata >>> Rionero in Vulture - Basilicata - Italy >>> >>> >>> 2014-02-21 18:53 GMT+01:00 Giovanni Calice >>> <giovcalice@gmail.com <mailto:giovcalice@gmail.com="">>: >>> >>> >>> > Hi Jim, >>> > >>> > Ok! >>> > My next bumphunter call will be on 1/3 of total ncores (I >>> share compute >>> > cycles with co-workers too) >>> > with cutoff and cutoffQ = 0.95. >>> > >>> > Many Thanks. >>> > >>> > Best, >>> > Giovanni >>> > >>> > Laboratory of Preclinical and Translational Research >>> > IRCCS - CROB Oncology Referral Center of Basilicata >>> > Rionero in Vulture - Basilicata - Italy >>> > >>> > >>> > >>> > 2014-02-21 18:29 GMT+01:00 James W. MacDonald >>> <jmacdon@uw.edu <mailto:jmacdon@uw.edu="">>: >>> >>> > >>> > Hi Giovanni, >>> >> >>> >> I don't know about the number of cores. I share compute >>> cycles with >>> >> co-workers, so can't just hog them all up. A recent >>> bumphunter run I did on >>> >> our shared server (a single multi-core machine with I >>> believe 32 >>> >> processors) was: >>> >> >>> >> library(doParallel) >>> >> registerDoParallel(cores = 12) >>> >> bmps.main <- bumphunter(eset, design.cd <http: design.cd="">, >>> >>> cutoff = 0.99) >>> >> >>> >> Which resulted in something like 2500 bumps and finished >>> in, I don't >>> >> know, say 15-20 minutes? >>> >> >>> >> Best, >>> >> >>> >> Jim >>> >> >>> >> >>> >> >>> >> On 2/21/2014 12:21 PM, Giovanni Calice wrote: >>> >> >>> >>> Hi Jim, >>> >>> >>> >>> the call for bumphunter is: >>> >>> >>> >>> bumphunter(myGenomicRatioSet, design=designMatrix, >>> cutoff=0.05, B=1000, >>> >>> verbose=TRUE) >>> >>> >>> >>> I set cutoff to 0.05 not cutoffQ. >>> >>> Next bumphunter call I will follow your advice; >>> >>> regard to parallelize the process what is your suggestion? >>> >>> >>> >>> Would it be better to parallelize only on some of the ncores? >>> >>> >>> >>> Best, >>> >>> Giovanni >>> >>> >>> >>> Laboratory of Preclinical and Translational Research >>> >>> IRCCS - CROB Oncology Referral Center of Basilicata >>> >>> Rionero in Vulture - Basilicata - Italy >>> >>> >>> >>> >>> >>> 2014-02-21 17:52 GMT+01:00 James W. MacDonald >>> <jmacdon@uw.edu <mailto:jmacdon@uw.edu=""> <mailto:>>> >>> >>> jmacdon@uw.edu <mailto:jmacdon@uw.edu>>>: >>> >>> >>> >>> >>> >>> Hi Giovanni, >>> >>> >>> >>> You should give the actual call you used for >>> bumphunter, rather >>> >>> than simply saying that you used 'recommended >>> parameters'. It >>> >>> looks like you set cutoffQ to 0.05, which is exactly >>> opposite to >>> >>> what you should be doing. Instead you should be using >>> something >>> >>> like cutoffQ = 0.95. >>> >>> >>> >>> Best, >>> >>> >>> >>> Jim >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On Friday, February 21, 2014 11:36:32 AM, Giovanni >>> Calice wrote: >>> >>> >>> >>> Hi Kasper, >>> >>> >>> >>> Thank you very much for the immediate response! >>> >>> >>> >>> So, >>> >>> What do you suggest? >>> >>> >>> >>> Giovanni >>> >>> >>> >>> Laboratory of Preclinical and Translational Research >>> >>> IRCCS - CROB Oncology Referral Center of Basilicata >>> >>> Rionero in Vulture - Basilicata - Italy >>> >>> >>> >>> >>> >>> 2014-02-21 17:27 GMT+01:00 Kasper Daniel Hansen >>> >>> <khansen@jhsph.edu <mailto:khansen@jhsph.edu=""> >>> <mailto:khansen@jhsph.edu <mailto:khansen@jhsph.edu="">>>: >>> >>> >>> >>> >>> >>> >>> >>> >>> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice >>> >>> <giovcalice@gmail.com>>> <mailto:giovcalice@gmail.com> <mailto:giovcalice@gmail.com>>> >>> <mailto:giovcalice@gmail.com>>>wrote: >>> >>> >>> >>> >>> >>> 273952 >>> >>> >>> >>> >>> >>> >>> >>> This is a crazy number of putative bumps >>> >>> >>> >>> Kasper >>> >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> >>> Bioconductor mailing list >>> >>> Bioconductor@r-project.org >>> <mailto:bioconductor@r-project.org> >>> <mailto:bioconductor@r-project.org>>> >>> <mailto:bioconductor@r-project.org>> >>> >>> >>> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> Search the archives: >>> >>> http://news.gmane.org/gmane.science.biology.informatics. >>> >>> conductor >>> >>> >>> >>> >>> >>> -- >>> >>> James W. MacDonald, M.S. >>> >>> Biostatistician >>> >>> University of Washington >>> >>> Environmental and Occupational Health Sciences >>> >>> 4225 Roosevelt Way NE, # 100 >>> >>> Seattle WA 98105-6099 >>> >>> >>> >>> >>> >>> >>> >> -- >>> >> James W. MacDonald, M.S. >>> >> Biostatistician >>> >> University of Washington >>> >> Environmental and Occupational Health Sciences >>> >> 4225 Roosevelt Way NE, # 100 >>> >> Seattle WA 98105-6099 >>> >> >>> >> >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics. >>> conductor >>> >>> >>> >>> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]