hi Mingfeng, Thanks for reporting this and sending the example. I found the bug that produced this hang, and just pushed v1.4.4 (available in 1 day on Bioc), which fixes this: > library(DESeq2) > load("~/Downloads/tmpFile.Rdata") > system.time({nbinomWaldTest(ddsMF)}) user system elapsed 14.841 0.777 15.634 # or the whole pipeline: > system.time({DESeq(ddsMF)}) using pre-existing normalization factors estimating dispersions you had estimated dispersions, replacing these gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing user system elapsed 38.768 1.457 40.240 Mike On Fri, May 9, 2014 at 5:38 PM, Mingfeng Li <mingfeng.li at="" yale.edu=""> wrote: > Hi Mike, > > Thanks your so fast response. I would like to send you one example in Rdata. > You can get the information of the design, the normalization factor matrix. > please reproduce the following codes: > library("DESeq2") > load("tmpFile.Rdata") > ddsMF = nbinomWaldTest(ddsMF); > > > Best, > Mingfeng > > > > > On Fri, May 9, 2014 at 4:12 PM, Michael Love <michaelisaiahlove at="" gmail.com=""> > wrote: >> >> hi Mingfeng, >> >> With 6 samples, this is typically seconds to run. If it's taking longer >> than a few minutes, usually this means something is wrong. Could you make a >> small reproducible example and send me data and a script? If this is not >> possible, I'd need some more information, like the code you are using, the >> design, the normalization factor matrix, etc. >> >> Mike >> >> >> On Fri, May 9, 2014 at 3:14 PM, Mingfeng [guest] <guest at="" bioconductor.org=""> >> wrote: >>> >>> >>> It is the exciting news of the coming of DESeq2. >>> There are many updates and incorporation with other software, e.g., Wald >>> test and cqn. >>> My question is the nbinomWaldTest may stuck running for long time when >>> using multiple factors, e.g., running several days but no results or >>> messages coming out. It works well when I remove the "type" factor. >>> I paste the meta data in the following: >>> condition type >>> S103 W U >>> S149 W Y >>> S114 W Y >>> S98 K U >>> S92 K U >>> S159 K Y >>> >>> >>> >>> >>> >>> >>> Thanks. >>> >>> >>> >>> >>> -- output of sessionInfo(): >>> >>> > sessionInfo() >>> R version 3.1.0 (2014-04-10) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] splines parallel stats graphics grDevices utils datasets >>> [8] methods base >>> >>> other attached packages: >>> [1] cqn_1.10.0 quantreg_5.05 SparseM_1.03 >>> [4] preprocessCore_1.26.0 nor1mix_1.1-4 mclust_4.3 >>> [7] DESeq2_1.4.1 RcppArmadillo_0.4.300.0 Rcpp_0.11.1 >>> [10] GenomicRanges_1.16.2 GenomeInfoDb_1.0.2 IRanges_1.22.4 >>> [13] BiocGenerics_0.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.26.0 Biobase_2.24.0 DBI_0.2-7 >>> [4] RColorBrewer_1.0-5 RSQLite_0.11.4 XML_3.98-1.1 >>> [7] XVector_0.4.0 annotate_1.42.0 genefilter_1.46.0 >>> [10] geneplotter_1.42.0 grid_3.1.0 lattice_0.20-29 >>> [13] locfit_1.5-9.1 stats4_3.1.0 survival_2.37-7 >>> [16] xtable_1.7-3 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >> >> > > > > -- > ********************************************* > Mingfeng Li, Ph.D. > Postdoctoral Associate > Department of Neurobiology > Yale University School of Medicine > 333 Cedar Street, SHM C-327C > New Haven, CT 06510 > > E-mail: mingfeng.li at yale.edu > Lab: (203) 785-5941 > Lab website: www.sestanlab.org > *********************************************

Just for users who end up on this thread through search: updating to DESeq2 v1.4.5 clears up this hang. Mike On Mon, May 12, 2014 at 1:11 PM, <lmf.bill at="" gmail.com=""> wrote: > Hi Mike, > I missed that email. Thank you very much. > > Best, > Mingfeng > > Sent from my iPod > > On May 12, 2014, at 12:34 PM, Michael Love <michaelisaiahlove at="" gmail.com=""> > wrote: > > hi Mingfeng, > > I sent a follow-up email that I forgot to bump the version number, and the > fix will be in 1.4.5, which should be out today. > > Mike > > > On Mon, May 12, 2014 at 12:03 PM, Mingfeng Li <mingfeng.li at="" yale.edu=""> wrote: >> >> Hi Mike, >> >> Thanks your help. Unfortunately, it does not work in my computer. It is >> still hanged when typing "system.time({nbinomWaldTest(ddsMF)})". I pasted >> the sessionInfo. Thanks. >> >> best, >> Mingfeng >> >> >> > sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] DESeq2_1.4.4 RcppArmadillo_0.4.300.0 Rcpp_0.11.1 >> [4] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 IRanges_1.22.6 >> [7] BiocGenerics_0.10.0 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.26.0 Biobase_2.24.0 DBI_0.2-7 >> [4] RColorBrewer_1.0-5 RSQLite_0.11.4 XML_3.98-1.1 >> [7] XVector_0.4.0 annotate_1.42.0 genefilter_1.46.1 >> [10] geneplotter_1.42.0 grid_3.1.0 lattice_0.20-29 >> [13] locfit_1.5-9.1 splines_3.1.0 stats4_3.1.0 >> [16] survival_2.37-7 xtable_1.7-3 >> >> >> >> On Sat, May 10, 2014 at 10:43 AM, Michael Love >> <michaelisaiahlove at="" gmail.com=""> wrote: >>> >>> hi Mingfeng, >>> >>> Thanks for reporting this and sending the example. I found the bug >>> that produced this hang, and just pushed v1.4.4 (available in 1 day on >>> Bioc), which fixes this: >>> >>> > library(DESeq2) >>> > load("~/Downloads/tmpFile.Rdata") >>> > system.time({nbinomWaldTest(ddsMF)}) >>> user system elapsed >>> 14.841 0.777 15.634 >>> >>> # or the whole pipeline: >>> >>> > system.time({DESeq(ddsMF)}) >>> using pre-existing normalization factors >>> estimating dispersions >>> you had estimated dispersions, replacing these >>> gene-wise dispersion estimates >>> mean-dispersion relationship >>> final dispersion estimates >>> fitting model and testing >>> user system elapsed >>> 38.768 1.457 40.240 >>> >>> Mike >>> >>> >>> On Fri, May 9, 2014 at 5:38 PM, Mingfeng Li <mingfeng.li at="" yale.edu=""> wrote: >>> > Hi Mike, >>> > >>> > Thanks your so fast response. I would like to send you one example in >>> > Rdata. >>> > You can get the information of the design, the normalization factor >>> > matrix. >>> > please reproduce the following codes: >>> > library("DESeq2") >>> > load("tmpFile.Rdata") >>> > ddsMF = nbinomWaldTest(ddsMF); >>> > >>> > >>> > Best, >>> > Mingfeng >>> > >>> > >>> > >>> > >>> > On Fri, May 9, 2014 at 4:12 PM, Michael Love >>> > <michaelisaiahlove at="" gmail.com=""> >>> > wrote: >>> >> >>> >> hi Mingfeng, >>> >> >>> >> With 6 samples, this is typically seconds to run. If it's taking >>> >> longer >>> >> than a few minutes, usually this means something is wrong. Could you >>> >> make a >>> >> small reproducible example and send me data and a script? If this is >>> >> not >>> >> possible, I'd need some more information, like the code you are using, >>> >> the >>> >> design, the normalization factor matrix, etc. >>> >> >>> >> Mike >>> >> >>> >> >>> >> On Fri, May 9, 2014 at 3:14 PM, Mingfeng [guest] >>> >> <guest at="" bioconductor.org=""> >>> >> wrote: >>> >>> >>> >>> >>> >>> It is the exciting news of the coming of DESeq2. >>> >>> There are many updates and incorporation with other software, e.g., >>> >>> Wald >>> >>> test and cqn. >>> >>> My question is the nbinomWaldTest may stuck running for long time >>> >>> when >>> >>> using multiple factors, e.g., running several days but no results or >>> >>> messages coming out. It works well when I remove the "type" factor. >>> >>> I paste the meta data in the following: >>> >>> condition type >>> >>> S103 W U >>> >>> S149 W Y >>> >>> S114 W Y >>> >>> S98 K U >>> >>> S92 K U >>> >>> S159 K Y >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> Thanks. >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -- output of sessionInfo(): >>> >>> >>> >>> > sessionInfo() >>> >>> R version 3.1.0 (2014-04-10) >>> >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> >>> >>> locale: >>> >>> [1] C >>> >>> >>> >>> attached base packages: >>> >>> [1] splines parallel stats graphics grDevices utils >>> >>> datasets >>> >>> [8] methods base >>> >>> >>> >>> other attached packages: >>> >>> [1] cqn_1.10.0 quantreg_5.05 SparseM_1.03 >>> >>> [4] preprocessCore_1.26.0 nor1mix_1.1-4 mclust_4.3 >>> >>> [7] DESeq2_1.4.1 RcppArmadillo_0.4.300.0 Rcpp_0.11.1 >>> >>> [10] GenomicRanges_1.16.2 GenomeInfoDb_1.0.2 IRanges_1.22.4 >>> >>> [13] BiocGenerics_0.10.0 >>> >>> >>> >>> loaded via a namespace (and not attached): >>> >>> [1] AnnotationDbi_1.26.0 Biobase_2.24.0 DBI_0.2-7 >>> >>> [4] RColorBrewer_1.0-5 RSQLite_0.11.4 XML_3.98-1.1 >>> >>> [7] XVector_0.4.0 annotate_1.42.0 genefilter_1.46.0 >>> >>> [10] geneplotter_1.42.0 grid_3.1.0 lattice_0.20-29 >>> >>> [13] locfit_1.5-9.1 stats4_3.1.0 survival_2.37-7 >>> >>> [16] xtable_1.7-3 >>> >>> >>> >>> -- >>> >>> Sent via the guest posting facility at bioconductor.org. >>> >> >>> >> >>> > >>> > >>> > >>> > -- >>> > ********************************************* >>> > Mingfeng Li, Ph.D. >>> > Postdoctoral Associate >>> > Department of Neurobiology >>> > Yale University School of Medicine >>> > 333 Cedar Street, SHM C-327C >>> > New Haven, CT 06510 >>> > >>> > E-mail: mingfeng.li at yale.edu >>> > Lab: (203) 785-5941 >>> > Lab website: www.sestanlab.org >>> > ********************************************* >> >> >> >> >> -- >> ********************************************* >> Mingfeng Li, Ph.D. >> Postdoctoral Associate >> Department of Neurobiology >> Yale University School of Medicine >> 333 Cedar Street, SHM C-327C >> New Haven, CT 06510 >> >> E-mail: mingfeng.li at yale.edu >> Lab: (203) 785-5941 >> Lab website: www.sestanlab.org >> ********************************************* > >