Question: DEXSeq- fitDispersionFunction error
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gravatar for Anitha Sundararajan
5.1 years ago by
Anitha Sundararajan140 wrote:
Hello- Has anyone seen the following error before with DEXSeq? I have run the tool a couple times before with no issues. So when I try to run the "fitDispersionFunction", I get the following: *no CR dispersion estimations found, please first call estimateDispersions function* I actually ran the estimateDispersions function prior to this without any problem. Thanks so much for your help. Anitha ===================================================== > 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] DEXSeq_1.8.0 Biobase_2.22.0 BiocGenerics_0.8.0 [4] BiocInstaller_1.12.1 loaded via a namespace (and not attached): [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 [4] GenomicRanges_1.14.4 hwriter_1.3 IRanges_1.20.7 [7] RCurl_1.95-4.1 Rsamtools_1.14.3 statmod_1.4.20 [10] stats4_3.0.2 stringr_0.6.2 tools_3.0.2 [13] XML_3.98-1.1 XVector_0.2.0 zlibbioc_1.8.0 [[alternative HTML version deleted]]
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ADD COMMENTlink written 5.1 years ago by Anitha Sundararajan140
Answer: DEXSeq- fitDispersionFunction error
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gravatar for Anitha Sundararajan
5.1 years ago by
Anitha Sundararajan140 wrote:
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ADD COMMENTlink written 5.1 years ago by Anitha Sundararajan140
This is a previous post that solved my problem, which might also help you. Best, Xiayu -----Original Message----- From: Alejandro Reyes [mailto:alejandro.reyes@embl.de] Sent: Tuesday, April 22, 2014 11:33 AM To: Rao,Xiayu; 'bioconductor at r-project.org' Subject: Re: dexseq fitDispersionFunction(ecs) error Dear Xiayu, Thanks for your report, we are looking into that right now, it has to do with versions of dependencies outside bioconductor. As a temporary solution, you can install an old version of statmod compatible with your version of DEXSeq by doing in your R session: library(devtools);install_url("http://cran.r-project.org/src/contrib/A rchive/statmod/statmod_1.4.18.tar.gz") Your code below should work then! Best regards, Alejandro -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Anitha Sundararajan Sent: Tuesday, July 29, 2014 3:32 PM To: bioconductor at r-project.org; bioconductor at stat.math.ethz.ch Subject: [BioC] DEXSeq- fitDispersionFunction error Hello- Has anyone seen the following error before with DEXSeq? I have run the tool a couple times before with no issues. So when I try to run the "fitDispersionFunction", I get the following: *no CR dispersion estimations found, please first call estimateDispersions function* I actually ran the estimateDispersions function prior to this without any problem. Thanks so much for your help. Anitha ===================================================== > 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] DEXSeq_1.8.0 Biobase_2.22.0 BiocGenerics_0.8.0 [4] BiocInstaller_1.12.1 loaded via a namespace (and not attached): [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 [4] GenomicRanges_1.14.4 hwriter_1.3 IRanges_1.20.7 [7] RCurl_1.95-4.1 Rsamtools_1.14.3 statmod_1.4.20 [10] stats4_3.0.2 stringr_0.6.2 tools_3.0.2 [13] XML_3.98-1.1 XVector_0.2.0 zlibbioc_1.8.0 [[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 5.1 years ago by Rao,Xiayu540
Please post the complete code, i.e., all the command that led up to the error message Simon On 29/07/14 22:31, Anitha Sundararajan wrote: > Hello- > > Has anyone seen the following error before with DEXSeq? I have run the > tool a couple times before with no issues. > > So when I try to run the "fitDispersionFunction", I get the following: > > *no CR dispersion estimations found, please first call > estimateDispersions function* > > I actually ran the estimateDispersions function prior to this without > any problem. > > Thanks so much for your help. > Anitha > > ===================================================== > > 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] DEXSeq_1.8.0 Biobase_2.22.0 BiocGenerics_0.8.0 > [4] BiocInstaller_1.12.1 > > loaded via a namespace (and not attached): > [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 > [4] GenomicRanges_1.14.4 hwriter_1.3 IRanges_1.20.7 > [7] RCurl_1.95-4.1 Rsamtools_1.14.3 statmod_1.4.20 > [10] stats4_3.0.2 stringr_0.6.2 tools_3.0.2 > [13] XML_3.98-1.1 XVector_0.2.0 zlibbioc_1.8.0 > > > [[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 5.1 years ago by Simon Anders3.6k
I re-ran some steps so you can see the output- Please see complete code below- ============================ >source("http://bioconductor.org/biocLite.R") >biocLite("DEXSeq") >library ("DEXSeq") >library("parallel") >sampleTable.conVsgigi <- data.frame (row.names=c("control1", "control2", "control3", "Gigi1", "Gigi2", "Gigi3"), countFile=c("/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotati on/DEXSeq/mt_root-1.counts", "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root-2.counts", "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root-3.counts", "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root_Gigi-1.counts", "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root_Gigi-2.counts", "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root_Gigi-3.counts"), condition=c("control", "control", "control", "Gigi", "Gigi", "Gigi"), stringsAsFactors=FALSE, check.names=FALSE) >sampleTable.conVsgigi countFile control1 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root-1.counts control2 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root-2.counts control3 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root-3.counts Gigi1 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root_Gigi-1.counts Gigi2 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root_Gigi-2.counts Gigi3 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root_Gigi-3.counts condition control1 control control2 control control3 control Gigi1 Gigi Gigi2 Gigi Gigi3 Gigi >file.exists(sampleTable.conVsgigi$countFile) >sapply (sampleTable.conVsgigi, class) >countFiles.conVsgigi <- sampleTable.conVsgigi$countFile >head (countFiles.conVsgigi) [1] "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root-1.counts" [2] "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root-2.counts" [3] "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root-3.counts" [4] "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root_Gigi-1.counts" [5] "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root_Gigi-2.counts" [6] "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt _root_Gigi-3.counts" >design.conVsgigi <- sampleTable.conVsgigi[,-1] >ecs.ConVsgigi <- read.HTSeqCounts (countFiles.conVsgigi, design.conVsgigi, "/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/Mt 4.0v1_genes_20130731_1800.Flattened.gff") >ecs.ConVsgigi ExonCountSet (storageMode: environment) assayData: 228882 features, 6 samples element names: counts protocolData: none phenoData sampleNames: /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root-1.counts /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root-2.counts ... /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root_Gigi-3.counts (6 total) varLabels: sizeFactor condition countfiles varMetadata: labelDescription featureData featureNames: Medtr0001s0010.1:E001 Medtr0001s0010.1:E002 ... Medtr8g494250.1:E002 (228882 total) fvarLabels: geneID exonID ... transcripts (13 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: >ecs.ConVsgigi.ESF <- estimateSizeFactors (ecs.ConVsgigi) >head (counts(ecs.ConVsgigi.ESF), normalized=TRUE) /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/m t_root-1.counts Medtr0001s0010.1:E001 0 Medtr0001s0010.1:E002 0 Medtr0001s0070.1:E001 0 Medtr0001s0100.1:E001 0 Medtr0001s0100.1:E002 0 Medtr0001s0120.1:E001 0 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root-2.counts Medtr0001s0010.1:E001 0 Medtr0001s0010.1:E002 0 Medtr0001s0070.1:E001 0 Medtr0001s0100.1:E001 0 Medtr0001s0100.1:E002 0 Medtr0001s0120.1:E001 0 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root-3.counts Medtr0001s0010.1:E001 0 Medtr0001s0010.1:E002 0 Medtr0001s0070.1:E001 0 Medtr0001s0100.1:E001 0 Medtr0001s0100.1:E002 0 Medtr0001s0120.1:E001 0 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root_Gigi-1.counts Medtr0001s0010.1:E001 0 Medtr0001s0010.1:E002 0 Medtr0001s0070.1:E001 0 Medtr0001s0100.1:E001 0 Medtr0001s0100.1:E002 0 Medtr0001s0120.1:E001 0 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root_Gigi-2.counts Medtr0001s0010.1:E001 0 Medtr0001s0010.1:E002 0 Medtr0001s0070.1:E001 0 Medtr0001s0100.1:E001 0 Medtr0001s0100.1:E002 0 Medtr0001s0120.1:E001 0 /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root_Gigi-3.counts Medtr0001s0010.1:E001 0 Medtr0001s0010.1:E002 0 Medtr0001s0070.1:E001 0 Medtr0001s0100.1:E001 0 Medtr0001s0100.1:E002 0 Medtr0001s0120.1:E001 0 >ecs.ConVsgigi.ED <- estimateDispersions (ecs.ConVsgigi.ESF, nCores=16) ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ........................................................ Done >head (ecs.ConVsgigi.ED) ExonCountSet (storageMode: environment) assayData: 1 features, 6 samples element names: counts protocolData: none phenoData sampleNames: /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root-1.counts /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root-2.counts ... /home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_ root_Gigi-3.counts (6 total) varLabels: sizeFactor countfiles condition varMetadata: labelDescription featureData featureNames: Medtr0001s0010.1:E001 fvarLabels: geneID exonID ... transcripts (13 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: >ecs.conVsgigi.FDF <- fitDispersionFunction (ecs.ConVsgigi.ED) Error in fitDispersionFunction(ecs.ConVsgigi.ED) : no CR dispersion estimations found, please first call estimateDispersions function ===================================================== Thanks Anitha On 7/29/14 2:34 PM, Simon Anders wrote: > Please post the complete code, i.e., all the command that led up to > the error message > > Simon > > On 29/07/14 22:31, Anitha Sundararajan wrote: >> Hello- >> >> Has anyone seen the following error before with DEXSeq? I have run the >> tool a couple times before with no issues. >> >> So when I try to run the "fitDispersionFunction", I get the following: >> >> *no CR dispersion estimations found, please first call >> estimateDispersions function* >> >> I actually ran the estimateDispersions function prior to this without >> any problem. >> >> Thanks so much for your help. >> Anitha >> >> ===================================================== >> > 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] DEXSeq_1.8.0 Biobase_2.22.0 BiocGenerics_0.8.0 >> [4] BiocInstaller_1.12.1 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 >> [4] GenomicRanges_1.14.4 hwriter_1.3 IRanges_1.20.7 >> [7] RCurl_1.95-4.1 Rsamtools_1.14.3 statmod_1.4.20 >> [10] stats4_3.0.2 stringr_0.6.2 tools_3.0.2 >> [13] XML_3.98-1.1 XVector_0.2.0 zlibbioc_1.8.0 >> >> >> [[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
ADD REPLYlink written 5.1 years ago by Anitha Sundararajan140
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