DEXSeq error
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Chuming Chen ▴ 140
@chuming-chen-3885
Last seen 9.6 years ago
Hi All, I am trying to use DEXSeq to find out differential exon usage and encounter the following error. I have included the session info and my R script. Could you please help me finding out what could be the problem? Estimating Cox-Reid exon dispersion estimates using 30 cores. (Progress report: one dot per 100 genes) ...................................................................... ..................................................Testing for differential exon usage using 30 cores. (Progress report: one dot per 100 genes) ...................................................................... ..................................................Error in pmax(which(decade_lengths > 0.1), 0) : cannot mix 0-length vectors with others The session info is below. > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DEXSeq_1.2.0 Biobase_2.16.0 BiocGenerics_0.2.0 multicore_0.1-7 loaded via a namespace (and not attached): [1] RCurl_1.91-1 XML_3.9-4 biomaRt_2.12.0 hwriter_1.3 plyr_1.7.1 [6] statmod_1.4.14 stringr_0.6 > My R script is below: $ more run-FL-LL-12-fdr-0.05.R library(multicore) library(DEXSeq) annotationfile = file.path("Gallus_gallus.WASHUC2.64.clc.gff") samples = data.frame( condition = c(rep("FL", 12), rep("LL", 12)), replicate = c(1:12, 1:12), row.names = dir("clcExonCountFiles", full.names=TRUE, pattern=".count"), stringsAsFactors = TRUE, check.names = FALSE ) ecs = read.HTSeqCounts(countfiles = file.path(rownames(samples)), design = samples, flattenedfile = annotationfile) ecs = estimateSizeFactors(ecs) ecs = estimateDispersions(ecs, nCores=30) ecs = fitDispersionFunction(ecs) ecs = testForDEU(ecs, nCores=30) DEXSeqHTML(ecs, geneIDs=NULL, path="report/FL-LL-12/FDR-0.05", file = "FL-LL-DEU-fdr0.05.html", fitExpToVar="condition", FDR=0.05, color=NULL, color.samples=NULL) [[alternative HTML version deleted]]
DEXSeq DEXSeq • 1.5k views
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Alejandro Reyes ★ 1.9k
@alejandro-reyes-5124
Last seen 6 months ago
Novartis Institutes for BioMedical Reseā€¦
Dear Chuming Chen, Thanks for the report, it was not so clear to me in which part of your code the error message comes out, but I think it is in DEXSeqHTML is that correct? I tried to reproduce an error with the line that appears there but I could not. Could you try updating to a newer version of DEXSeq? Or could you send me your ecs (or a subset of it containing the gene that generates that error)? Alejandro Reyes > Hi All, > > I am trying to use DEXSeq to find out differential exon usage and encounter the following error. I have included the session info and my R script. > > Could you please help me finding out what could be the problem? > > > Estimating Cox-Reid exon dispersion estimates using 30 cores. (Progress report: one dot per 100 genes) > .................................................................... ....................................................Testing for differential exon usage using 30 cores. (Progress report: one dot per 100 genes) > .................................................................... ....................................................Error in pmax(which(decade_lengths > 0.1), 0) : > cannot mix 0-length vectors with others > > The session info is below. >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DEXSeq_1.2.0 Biobase_2.16.0 BiocGenerics_0.2.0 multicore_0.1-7 > > loaded via a namespace (and not attached): > [1] RCurl_1.91-1 XML_3.9-4 biomaRt_2.12.0 hwriter_1.3 plyr_1.7.1 > [6] statmod_1.4.14 stringr_0.6 >> > > My R script is below: > $ more run-FL-LL-12-fdr-0.05.R > library(multicore) > library(DEXSeq) > annotationfile = file.path("Gallus_gallus.WASHUC2.64.clc.gff") > samples = data.frame( > condition = c(rep("FL", 12), rep("LL", 12)), > replicate = c(1:12, 1:12), > row.names = dir("clcExonCountFiles", full.names=TRUE, pattern=".count"), > stringsAsFactors = TRUE, > check.names = FALSE > ) > ecs = read.HTSeqCounts(countfiles = file.path(rownames(samples)), design = samples, flattenedfile = annotationfile) > ecs = estimateSizeFactors(ecs) > ecs = estimateDispersions(ecs, nCores=30) > ecs = fitDispersionFunction(ecs) > ecs = testForDEU(ecs, nCores=30) > DEXSeqHTML(ecs, geneIDs=NULL, path="report/FL-LL-12/FDR-0.05", file = "FL-LL-DEU-fdr0.05.html", fitExpToVar="condition", FDR=0.05, color=NULL, color.samples=NULL) > [[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 >
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Hi Alejandro, Thanks a lot for your quick reply! Please see my answers to your questions below. On Jul 6, 2012, at 12:33 PM, Alejandro Reyes wrote: > Dear Chuming Chen, > > Thanks for the report, it was not so clear to me in which part of your code the error message comes out, but I think it is in DEXSeqHTML is that correct? Yes. It is in DEXSeqHTML step. Actually, the image files and related html files have been created in the "files" folder. But the summary table on the FL-LL-DEU-fdr0.05.html were not created. > I tried to reproduce an error with the line that appears there but I could not. Could you try updating to a newer version of DEXSeq? I am using DEXSeq_1.2.0. Is this the latest version? Where can I get the newer version? > Or could you send me your ecs (or a subset of it containing the gene that generates that error)? > You can find my ecs at http://www.eecis.udel.edu/~chenc/DEXSeq/ecs.Rdata Thanks again. Chuming > Alejandro Reyes > > > >> Hi All, >> >> I am trying to use DEXSeq to find out differential exon usage and encounter the following error. I have included the session info and my R script. >> >> Could you please help me finding out what could be the problem? >> >> >> Estimating Cox-Reid exon dispersion estimates using 30 cores. (Progress report: one dot per 100 genes) >> ................................................................... .....................................................Testing for differential exon usage using 30 cores. (Progress report: one dot per 100 genes) >> ................................................................... .....................................................Error in pmax(which(decade_lengths > 0.1), 0) : >> cannot mix 0-length vectors with others >> >> The session info is below. >>> sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] DEXSeq_1.2.0 Biobase_2.16.0 BiocGenerics_0.2.0 multicore_0.1-7 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.91-1 XML_3.9-4 biomaRt_2.12.0 hwriter_1.3 plyr_1.7.1 >> [6] statmod_1.4.14 stringr_0.6 >>> >> >> My R script is below: >> $ more run-FL-LL-12-fdr-0.05.R >> library(multicore) >> library(DEXSeq) >> annotationfile = file.path("Gallus_gallus.WASHUC2.64.clc.gff") >> samples = data.frame( >> condition = c(rep("FL", 12), rep("LL", 12)), >> replicate = c(1:12, 1:12), >> row.names = dir("clcExonCountFiles", full.names=TRUE, pattern=".count"), >> stringsAsFactors = TRUE, >> check.names = FALSE >> ) >> ecs = read.HTSeqCounts(countfiles = file.path(rownames(samples)), design = samples, flattenedfile = annotationfile) >> ecs = estimateSizeFactors(ecs) >> ecs = estimateDispersions(ecs, nCores=30) >> ecs = fitDispersionFunction(ecs) >> ecs = testForDEU(ecs, nCores=30) >> DEXSeqHTML(ecs, geneIDs=NULL, path="report/FL-LL-12/FDR-0.05", file = "FL-LL-DEU-fdr0.05.html", fitExpToVar="condition", FDR=0.05, color=NULL, color.samples=NULL) >> [[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 >> > >
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Dear Chuming Thank you for your message. The current version of DEXSeq is 1.3.9: http://www.bioconductor.org/packages/devel/bioc/html/DEXSeq.html Can you try again with that, and report to us if the error persists? Best wishes Wolfgang On 7/6/12 9:33 PM, Chuming Chen wrote: > Hi Alejandro, > > Thanks a lot for your quick reply! Please see my answers to your questions below. > > On Jul 6, 2012, at 12:33 PM, Alejandro Reyes wrote: > >> Dear Chuming Chen, >> >> Thanks for the report, it was not so clear to me in which part of your code the error message comes out, but I think it is in DEXSeqHTML is that correct? > > Yes. It is in DEXSeqHTML step. Actually, the image files and related html files have been created in the "files" folder. But the summary table on the FL-LL-DEU-fdr0.05.html were not created. > >> I tried to reproduce an error with the line that appears there but I could not. Could you try updating to a newer version of DEXSeq? > > I am using DEXSeq_1.2.0. Is this the latest version? Where can I get the newer version? > > >> Or could you send me your ecs (or a subset of it containing the gene that generates that error)? >> > > You can find my ecs at http://www.eecis.udel.edu/~chenc/DEXSeq/ecs.Rdata > > > Thanks again. > > Chuming > >> Alejandro Reyes >> >> >> >>> Hi All, >>> >>> I am trying to use DEXSeq to find out differential exon usage and encounter the following error. I have included the session info and my R script. >>> >>> Could you please help me finding out what could be the problem? >>> >>> >>> Estimating Cox-Reid exon dispersion estimates using 30 cores. (Progress report: one dot per 100 genes) >>> .................................................................. ......................................................Testing for differential exon usage using 30 cores. (Progress report: one dot per 100 genes) >>> .................................................................. ......................................................Error in pmax(which(decade_lengths> 0.1), 0) : >>> cannot mix 0-length vectors with others >>> >>> The session info is below. >>>> sessionInfo() >>> R version 2.15.0 (2012-03-30) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] DEXSeq_1.2.0 Biobase_2.16.0 BiocGenerics_0.2.0 multicore_0.1-7 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_1.91-1 XML_3.9-4 biomaRt_2.12.0 hwriter_1.3 plyr_1.7.1 >>> [6] statmod_1.4.14 stringr_0.6 >>>> >>> >>> My R script is below: >>> $ more run-FL-LL-12-fdr-0.05.R >>> library(multicore) >>> library(DEXSeq) >>> annotationfile = file.path("Gallus_gallus.WASHUC2.64.clc.gff") >>> samples = data.frame( >>> condition = c(rep("FL", 12), rep("LL", 12)), >>> replicate = c(1:12, 1:12), >>> row.names = dir("clcExonCountFiles", full.names=TRUE, pattern=".count"), >>> stringsAsFactors = TRUE, >>> check.names = FALSE >>> ) >>> ecs = read.HTSeqCounts(countfiles = file.path(rownames(samples)), design = samples, flattenedfile = annotationfile) >>> ecs = estimateSizeFactors(ecs) >>> ecs = estimateDispersions(ecs, nCores=30) >>> ecs = fitDispersionFunction(ecs) >>> ecs = testForDEU(ecs, nCores=30) >>> DEXSeqHTML(ecs, geneIDs=NULL, path="report/FL-LL-12/FDR-0.05", file = "FL-LL-DEU-fdr0.05.html", fitExpToVar="condition", FDR=0.05, color=NULL, color.samples=NULL) >>> [[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 >>> >> >> > > _______________________________________________ > 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 -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Dear Wolfgang, I have downloaded DEXSeq 1.3.9 and tested using my data. Everything is fine now. Thanks for this nice tools and quick fix. Chuming On Jul 12, 2012, at 7:57 AM, Wolfgang Huber wrote: > Dear Chuming > > Thank you for your message. The current version of DEXSeq is 1.3.9: > http://www.bioconductor.org/packages/devel/bioc/html/DEXSeq.html > > Can you try again with that, and report to us if the error persists? > > Best wishes > Wolfgang > > On 7/6/12 9:33 PM, Chuming Chen wrote: >> Hi Alejandro, >> >> Thanks a lot for your quick reply! Please see my answers to your questions below. >> >> On Jul 6, 2012, at 12:33 PM, Alejandro Reyes wrote: >> >>> Dear Chuming Chen, >>> >>> Thanks for the report, it was not so clear to me in which part of your code the error message comes out, but I think it is in DEXSeqHTML is that correct? >> >> Yes. It is in DEXSeqHTML step. Actually, the image files and related html files have been created in the "files" folder. But the summary table on the FL-LL-DEU-fdr0.05.html were not created. >> >>> I tried to reproduce an error with the line that appears there but I could not. Could you try updating to a newer version of DEXSeq? >> >> I am using DEXSeq_1.2.0. Is this the latest version? Where can I get the newer version? >> >> >>> Or could you send me your ecs (or a subset of it containing the gene that generates that error)? >>> >> >> You can find my ecs at http://www.eecis.udel.edu/~chenc/DEXSeq/ecs.Rdata >> >> >> Thanks again. >> >> Chuming >> >>> Alejandro Reyes >>> >>> >>> >>>> Hi All, >>>> >>>> I am trying to use DEXSeq to find out differential exon usage and encounter the following error. I have included the session info and my R script. >>>> >>>> Could you please help me finding out what could be the problem? >>>> >>>> >>>> Estimating Cox-Reid exon dispersion estimates using 30 cores. (Progress report: one dot per 100 genes) >>>> ................................................................. .......................................................Testing for differential exon usage using 30 cores. (Progress report: one dot per 100 genes) >>>> ................................................................. .......................................................Error in pmax(which(decade_lengths> 0.1), 0) : >>>> cannot mix 0-length vectors with others >>>> >>>> The session info is below. >>>>> sessionInfo() >>>> R version 2.15.0 (2012-03-30) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] DEXSeq_1.2.0 Biobase_2.16.0 BiocGenerics_0.2.0 multicore_0.1-7 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] RCurl_1.91-1 XML_3.9-4 biomaRt_2.12.0 hwriter_1.3 plyr_1.7.1 >>>> [6] statmod_1.4.14 stringr_0.6 >>>>> >>>> >>>> My R script is below: >>>> $ more run-FL-LL-12-fdr-0.05.R >>>> library(multicore) >>>> library(DEXSeq) >>>> annotationfile = file.path("Gallus_gallus.WASHUC2.64.clc.gff") >>>> samples = data.frame( >>>> condition = c(rep("FL", 12), rep("LL", 12)), >>>> replicate = c(1:12, 1:12), >>>> row.names = dir("clcExonCountFiles", full.names=TRUE, pattern=".count"), >>>> stringsAsFactors = TRUE, >>>> check.names = FALSE >>>> ) >>>> ecs = read.HTSeqCounts(countfiles = file.path(rownames(samples)), design = samples, flattenedfile = annotationfile) >>>> ecs = estimateSizeFactors(ecs) >>>> ecs = estimateDispersions(ecs, nCores=30) >>>> ecs = fitDispersionFunction(ecs) >>>> ecs = testForDEU(ecs, nCores=30) >>>> DEXSeqHTML(ecs, geneIDs=NULL, path="report/FL-LL-12/FDR-0.05", file = "FL-LL-DEU-fdr0.05.html", fitExpToVar="condition", FDR=0.05, color=NULL, color.samples=NULL) >>>> [[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 >>>> >>> >>> >> >> _______________________________________________ >> 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 > > > -- > Best wishes > Wolfgang > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > 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
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