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Question: DEXSeq error
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gravatar for Chuming Chen
5.4 years ago by
Chuming Chen140
Chuming Chen140 wrote:
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]]
ADD COMMENTlink modified 5.4 years ago by Alejandro Reyes1.5k • written 5.4 years ago by Chuming Chen140
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gravatar for Alejandro Reyes
5.4 years ago by
Alejandro Reyes1.5k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.5k 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? 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 >
ADD COMMENTlink written 5.4 years ago by Alejandro Reyes1.5k
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 >> > >
ADD REPLYlink written 5.4 years ago by Chuming Chen140
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
ADD REPLYlink written 5.4 years ago by Wolfgang Huber13k
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
ADD REPLYlink written 5.4 years ago by Chuming Chen140
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