bumphunter DMRs difficulties
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@giovanni-calice-6415
Last seen 16 months ago
Italy
Hi Bioconductor Developers and Users, I'm using Minfi package 1.8.9 to analyze .IDAT files of Illumina 450k chip. I've implemented my pipeline to process data and to execute custom filters and so my goal now is focused to obtain DMRs by bumphunter-methods seen that minfi package interfaces with bumphunter package. When I start the bumphunter method with the reccomended parameters by the reference manual (B=1000 and parallelized process with other package like doParallel), the system has a performance decrease making it necessary to kill process and reboot the system if the parallelism is to all ncores or the bumphunter method hangs without producing results. Is there an estimation of the execution time for results relating DMRs? Is there an estimation of the storage space (temp and caching included)? Is to large the dataset (also if first I considered all 12 samples then I reduced the number to 4 samples)? Would it be better to parallelize only on some of the ncores? ***** Output and sessionInfo ***** class: GenomicRatioSet dim: 473462 4 exptData(0): assays(3): Beta M CN rownames(473462): cg13869341 cg14008030 ... cg07660283 cg09226288 rowData metadata column names(0): colnames(4): 9344737133_R03C01 9344737133_R01C02 9344737133_R04C01 9344737133_R02C02 colData names(9): Sample_Name Sample_Well ... Basename filenames Annotation array: IlluminaHumanMethylation450k annotation: ilmn12.hg19 Preprocessing Method: SWAN (based on a MethylSet preprocesses as 'Raw (no normalization or bg correction)' minfi version: 1.8.9 Manifest version: 0.4.0 [bumphunterEngine] Computing coefficients. [bumphunterEngine] Performing 1000 permutations. [bumphunterEngine] Computing marginal permutation p-values. [bumphunterEngine] cutoff: 0.05 [bumphunterEngine] Finding regions. [bumphunterEngine] Found 273952 bumps. [bumphunterEngine] Computing regions for each permutation. Loading required package: rngtools Loading required package: pkgmaker Loading required package: registry Attaching package: 'pkgmaker' The following object is masked from 'package:IRanges': new2 [bumphunterEngine] Estimating p-values and FWER. > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] doParallel_1.0.6 doRNG_1.5.5 rngtools_1.2.3 [4] pkgmaker_0.17.4 registry_0.2 minfi_1.8.9 [7] bumphunter_1.2.0 locfit_1.5-9.1 iterators_1.0.6 [10] foreach_1.4.1 Biostrings_2.30.1 GenomicRanges_1.14.4 [13] XVector_0.2.0 IRanges_1.20.6 reshape_0.8.4 [16] plyr_1.8 lattice_0.20-24 Biobase_2.22.0 [19] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationDbi_1.24.0 base64_1.1 [4] beanplot_1.1 codetools_0.2-8 compiler_3.0.2 [7] DBI_0.2-7 digest_0.6.4 genefilter_1.44.0 [10] grid_3.0.2 illuminaio_0.4.0 itertools_0.1-1 [13] limma_3.18.11 MASS_7.3-29 matrixStats_0.8.14 [16] mclust_4.2 multtest_2.18.0 nlme_3.1-113 [19] nor1mix_1.1-4 preprocessCore_1.24.0 RColorBrewer_1.0-5 [22] R.methodsS3_1.6.1 RSQLite_0.11.4 siggenes_1.36.0 [25] splines_3.0.2 stats4_3.0.2 stringr_0.6.2 [28] survival_2.37-7 tools_3.0.2 XML_3.98-1.1 [31] xtable_1.7-1 > ***** End Output and sessionInfo ***** Server Specifications/Features: PowerEdge R910 Server Processor 2x Intel Xeon E7-4860 Additional processor 2x Intel Xeon E7-4860 Memory 64GB Red Hat Enterprise Linux Server 6.5 Thanks in advance, Giovanni Laboratory of Preclinical and Translational Research IRCCS - CROB Oncology Referral Center of Basilicata Rionero in Vulture - Basilicata - Italy [[alternative HTML version deleted]]
PROcess minfi bumphunter PROcess minfi bumphunter • 2.0k views
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@kasper-daniel-hansen-2979
Last seen 10 months ago
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On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice <giovcalice@gmail.com>wrote: > 273952 This is a crazy number of putative bumps Kasper [[alternative HTML version deleted]]
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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>: > > On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice <giovcalice@gmail.com>wrote: > >> 273952 > > > This is a crazy number of putative bumps > > Kasper > [[alternative HTML version deleted]]
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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 at="" jhsph.edu="">: > >> >> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice <giovcalice at="" gmail.com="">wrote: >> >>> 273952 >> >> >> This is a crazy number of putative bumps >> >> Kasper >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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
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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>: > 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>: >> >> >>> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice <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 >> 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 > [[alternative HTML version deleted]]
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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, 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 at="" uw.edu=""> <mailto:jmacdon at="" 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 at="" jhsph.edu="" <mailto:khansen="" at="" jhsph.edu="">>: > > > On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice > <giovcalice at="" gmail.com="" <mailto:giovcalice="" at="" gmail.com="">>wrote: > > 273952 > > > > This is a crazy number of putative bumps > > Kasper > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" 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
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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>: > 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, 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>>: >> >> >> 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="">>: >> >> >> >> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice >> <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> >> >> 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]]
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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>: > 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>: > > 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, 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>>: >>> >>> >>> 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="">>: >>> >>> >>> >>> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice >>> <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> >>> >>> 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]]
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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>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>: > > > 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>: > > > > 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, 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>>: > >>> > >>> > >>> 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="">>: > >>> > >>> > >>> > >>> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice > >>> <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> > >>> > >>> 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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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>: > 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>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>: >> >> > 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>: >> > >> > 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, 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>>: >> >>> >> >>> >> >>> 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="">>: >> >>> >> >>> >> >>> >> >>> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice >> >>> <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>> > >> >>> >> >>> 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 >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
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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 at="" gmail.com=""> <mailto:tim.triche at="" 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 at="" gmail.com="" <mailto:giovcalice="" at="" 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 at="" gmail.com="" <mailto:giovcalice="" at="" 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 at="" uw.edu="" <mailto:jmacdon="" at="" 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 at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> <mailto:> >>> jmacdon at uw.edu <mailto:jmacdon at="" 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 at="" jhsph.edu="" <mailto:khansen="" at="" jhsph.edu=""> > <mailto:khansen at="" jhsph.edu="" <mailto:khansen="" at="" jhsph.edu="">>>: > >>> > >>> > >>> > >>> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice > >>> <giovcalice at="" gmail.com=""> <mailto:giovcalice at="" gmail.com=""> <mailto:giovcalice at="" gmail.com=""> <mailto:giovcalice at="" gmail.com="">>>wrote: > >>> > >>> > >>> 273952 > >>> > >>> > >>> > >>> This is a crazy number of putative bumps > >>> > >>> Kasper > >>> > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at r-project.org > <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org=""> <mailto:bioconductor at="" 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 at r-project.org <mailto:bioconductor at="" 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
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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]]
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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]]
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