DEXSeq package: Error in DEXSeqHTML
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Ahmet ZEHIR ▴ 50
@ahmet-zehir-5159
Last seen 10.3 years ago
Dear list, I am using DEXseq to look at differential exon usage and everything seems to work just fine. When I want to create an HTML report however, I get the following error: > DEXSeqHTML(ecsA673vshMSC, FDR = 0.001, color = c("#FF000080", "#0000FF80")) Error in plot.new() : figure margins too large In addition: Warning message: In plotDEXSeq(ecs, geneID = gene, FDR = FDR, lwd = 2, expression = opts[1], : This gene contains more than 42 transcripts annotated, only the first 42 will be plotted After this error, the function quits and the output is not complete. Is there a way to turn this message off and continue outputting the rest of the HTML report? Thanks, > sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/en_US.UTF-8/C/C/C/C attached base packages: [1] grDevices datasets splines graphics utils grid stats methods base other attached packages: [1] edgeR_2.4.6 limma_3.10.3 biomaRt_2.10.0 DEXSeq_1.0.2 Biobase_2.14.0 plyr_1.7.1 reshape2_1.2.1 [8] survival_2.36-14 RSQLite_0.11.1 DBI_0.2-5 knitr_0.5 gplots_2.10.1 KernSmooth_2.23-7 caTools_1.12 [15] bitops_1.0-4.1 gdata_2.8.2 gtools_2.6.2 RColorBrewer_1.0-5 ggplot2_0.9.1 loaded via a namespace (and not attached): [1] MASS_7.3-18 RCurl_1.91-1 Rcpp_0.9.10 XML_3.9-4 codetools_0.2-8 colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 [9] evaluate_0.4.2 formatR_0.4 highlight_0.3.1 hwriter_1.3 labeling_0.1 memoise_0.1 munsell_0.3 parser_0.0-14 [17] proto_0.3-9.2 scales_0.2.1 statmod_1.4.14 stringr_0.6 tools_2.14.2 -- *Ahmet Z.* [[alternative HTML version deleted]]
DEXSeq DEXSeq • 1.5k views
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Alejandro Reyes ★ 1.9k
@alejandro-reyes-5124
Last seen 5 months ago
Novartis Institutes for BioMedical Rese…
Dear Ahmet, Thanks for your report! You are using a quite old version of DEXSeq (1.0.2), I would recommend you try updating to one of the most recent versions, both in the current stable or the current devel this should not be a problem any more.Let me know if its not the case. Best wishes, Alejandro > Dear list, > > I am using DEXseq to look at differential exon usage and everything seems > to work just fine. When I want to create an HTML report however, I get the > following error: > >> DEXSeqHTML(ecsA673vshMSC, FDR = 0.001, color = c("#FF000080", > "#0000FF80")) > Error in plot.new() : figure margins too large > In addition: Warning message: > In plotDEXSeq(ecs, geneID = gene, FDR = FDR, lwd = 2, expression = opts[1], > : > This gene contains more than 42 transcripts annotated, only the first 42 > will be plotted > > After this error, the function quits and the output is not complete. Is > there a way to turn this message off and continue outputting the rest of > the HTML report? > > Thanks, > >> sessionInfo() > R version 2.14.2 (2012-02-29) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/en_US.UTF-8/C/C/C/C > > attached base packages: > [1] grDevices datasets splines graphics utils grid stats > methods base > > other attached packages: > [1] edgeR_2.4.6 limma_3.10.3 biomaRt_2.10.0 DEXSeq_1.0.2 > Biobase_2.14.0 plyr_1.7.1 reshape2_1.2.1 > [8] survival_2.36-14 RSQLite_0.11.1 DBI_0.2-5 knitr_0.5 > gplots_2.10.1 KernSmooth_2.23-7 caTools_1.12 > [15] bitops_1.0-4.1 gdata_2.8.2 gtools_2.6.2 > RColorBrewer_1.0-5 ggplot2_0.9.1 > > loaded via a namespace (and not attached): > [1] MASS_7.3-18 RCurl_1.91-1 Rcpp_0.9.10 XML_3.9-4 > codetools_0.2-8 colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 > [9] evaluate_0.4.2 formatR_0.4 highlight_0.3.1 hwriter_1.3 > labeling_0.1 memoise_0.1 munsell_0.3 parser_0.0-14 > [17] proto_0.3-9.2 scales_0.2.1 statmod_1.4.14 stringr_0.6 > tools_2.14.2 >
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Dear Alejandro, I think back in the day I installed DEXSeq through NCI's mirror and it seems like the package is not updated there. I'm assuming that's why I missed the updates (here 1.0.2 is cited as the current version: http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.ht ml) I will update to 1.2 right away. Thanks for your reply! Cheers, Ahmet Z. On Tue, Jun 5, 2012 at 4:17 AM, Alejandro Reyes <alejandro.reyes@embl.de>wrote: > Dear Ahmet, > > Thanks for your report! > You are using a quite old version of DEXSeq (1.0.2), I would recommend you > try updating to one of the most recent versions, both in the current stable > or the current devel this should not be a problem any more.Let me know if > its not the case. > > Best wishes, > Alejandro > > > > Dear list, >> >> I am using DEXseq to look at differential exon usage and everything seems >> to work just fine. When I want to create an HTML report however, I get the >> following error: >> >> DEXSeqHTML(ecsA673vshMSC, FDR = 0.001, color = c("#FF000080", >>> >> "#0000FF80")) >> Error in plot.new() : figure margins too large >> In addition: Warning message: >> In plotDEXSeq(ecs, geneID = gene, FDR = FDR, lwd = 2, expression = >> opts[1], >> : >> This gene contains more than 42 transcripts annotated, only the first 42 >> will be plotted >> >> After this error, the function quits and the output is not complete. Is >> there a way to turn this message off and continue outputting the rest of >> the HTML report? >> >> Thanks, >> >> sessionInfo() >>> >> R version 2.14.2 (2012-02-29) >> Platform: x86_64-apple-darwin9.8.0/x86_**64 (64-bit) >> >> locale: >> [1] C/en_US.UTF-8/C/C/C/C >> >> attached base packages: >> [1] grDevices datasets splines graphics utils grid stats >> methods base >> >> other attached packages: >> [1] edgeR_2.4.6 limma_3.10.3 biomaRt_2.10.0 DEXSeq_1.0.2 >> Biobase_2.14.0 plyr_1.7.1 reshape2_1.2.1 >> [8] survival_2.36-14 RSQLite_0.11.1 DBI_0.2-5 knitr_0.5 >> gplots_2.10.1 KernSmooth_2.23-7 caTools_1.12 >> [15] bitops_1.0-4.1 gdata_2.8.2 gtools_2.6.2 >> RColorBrewer_1.0-5 ggplot2_0.9.1 >> >> loaded via a namespace (and not attached): >> [1] MASS_7.3-18 RCurl_1.91-1 Rcpp_0.9.10 XML_3.9-4 >> codetools_0.2-8 colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 >> [9] evaluate_0.4.2 formatR_0.4 highlight_0.3.1 hwriter_1.3 >> labeling_0.1 memoise_0.1 munsell_0.3 parser_0.0-14 >> [17] proto_0.3-9.2 scales_0.2.1 statmod_1.4.14 stringr_0.6 >> tools_2.14.2 >> >> > -- *Ahmet Z.* [[alternative HTML version deleted]]
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oh, I just typed this: source("http://bioconductor.org/biocLite.R") biocLite("DEXSeq") It installed 1.0.2 again. I'll download the updated version and install it manually but something might be broken there. (I check for package updates frequently and DEXSeq never updated there either) Ahmet On Tue, Jun 5, 2012 at 9:39 AM, Ahmet ZEHIR <ahmetzehir@gmail.com> wrote: > Dear Alejandro, > > I think back in the day I installed DEXSeq through NCI's mirror and it > seems like the package is not updated there. I'm assuming that's why I > missed the updates (here 1.0.2 is cited as the current version: > http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq. html) > > I will update to 1.2 right away. Thanks for your reply! > > Cheers, > > Ahmet Z. > > > On Tue, Jun 5, 2012 at 4:17 AM, Alejandro Reyes <alejandro.reyes@embl.de>wrote: > >> Dear Ahmet, >> >> Thanks for your report! >> You are using a quite old version of DEXSeq (1.0.2), I would recommend >> you try updating to one of the most recent versions, both in the current >> stable or the current devel this should not be a problem any more.Let me >> know if its not the case. >> >> Best wishes, >> Alejandro >> >> >> >> Dear list, >>> >>> I am using DEXseq to look at differential exon usage and everything seems >>> to work just fine. When I want to create an HTML report however, I get >>> the >>> following error: >>> >>> DEXSeqHTML(ecsA673vshMSC, FDR = 0.001, color = c("#FF000080", >>>> >>> "#0000FF80")) >>> Error in plot.new() : figure margins too large >>> In addition: Warning message: >>> In plotDEXSeq(ecs, geneID = gene, FDR = FDR, lwd = 2, expression = >>> opts[1], >>> : >>> This gene contains more than 42 transcripts annotated, only the first >>> 42 >>> will be plotted >>> >>> After this error, the function quits and the output is not complete. Is >>> there a way to turn this message off and continue outputting the rest of >>> the HTML report? >>> >>> Thanks, >>> >>> sessionInfo() >>>> >>> R version 2.14.2 (2012-02-29) >>> Platform: x86_64-apple-darwin9.8.0/x86_**64 (64-bit) >>> >>> locale: >>> [1] C/en_US.UTF-8/C/C/C/C >>> >>> attached base packages: >>> [1] grDevices datasets splines graphics utils grid stats >>> methods base >>> >>> other attached packages: >>> [1] edgeR_2.4.6 limma_3.10.3 biomaRt_2.10.0 >>> DEXSeq_1.0.2 >>> Biobase_2.14.0 plyr_1.7.1 reshape2_1.2.1 >>> [8] survival_2.36-14 RSQLite_0.11.1 DBI_0.2-5 knitr_0.5 >>> gplots_2.10.1 KernSmooth_2.23-7 caTools_1.12 >>> [15] bitops_1.0-4.1 gdata_2.8.2 gtools_2.6.2 >>> RColorBrewer_1.0-5 ggplot2_0.9.1 >>> >>> loaded via a namespace (and not attached): >>> [1] MASS_7.3-18 RCurl_1.91-1 Rcpp_0.9.10 XML_3.9-4 >>> codetools_0.2-8 colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 >>> [9] evaluate_0.4.2 formatR_0.4 highlight_0.3.1 hwriter_1.3 >>> labeling_0.1 memoise_0.1 munsell_0.3 parser_0.0-14 >>> [17] proto_0.3-9.2 scales_0.2.1 statmod_1.4.14 stringr_0.6 >>> tools_2.14.2 >>> >>> >> > > > -- > *Ahmet Z.* > -- *Ahmet Z.* [[alternative HTML version deleted]]
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Dear Ahmet, It depends on the R version you are using, 1.0.2 is the release for the R version you are using (2.14.2), if you update your R to a newest version and install it again via "biocLite", it will install the newest version of DEXSeq. Best wishes, Alejandro > oh, I just typed this: > > > source("http://bioconductor.org/biocLite.R") > biocLite("DEXSeq") > > It installed 1.0.2 again. I'll download the updated version and install > it manually but something might be broken there. (I check for package > updates frequently and DEXSeq never updated there either) > > > Ahmet > On Tue, Jun 5, 2012 at 9:39 AM, Ahmet ZEHIR <ahmetzehir at="" gmail.com=""> <mailto:ahmetzehir at="" gmail.com="">> wrote: > > Dear Alejandro, > > I think back in the day I installed DEXSeq through NCI's mirror and > it seems like the package is not updated there. I'm assuming that's > why I missed the updates (here 1.0.2 is cited as the current > version: > http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEX Seq.html) > > I will update to 1.2 right away. Thanks for your reply! > > Cheers, > > Ahmet Z. > > > On Tue, Jun 5, 2012 at 4:17 AM, Alejandro Reyes > <alejandro.reyes at="" embl.de="" <mailto:alejandro.reyes="" at="" embl.de="">> wrote: > > Dear Ahmet, > > Thanks for your report! > You are using a quite old version of DEXSeq (1.0.2), I would > recommend you try updating to one of the most recent versions, > both in the current stable or the current devel this should not > be a problem any more.Let me know if its not the case. > > Best wishes, > Alejandro > > > > Dear list, > > I am using DEXseq to look at differential exon usage and > everything seems > to work just fine. When I want to create an HTML report > however, I get the > following error: > > DEXSeqHTML(ecsA673vshMSC, FDR = 0.001, color = > c("#FF000080", > > "#0000FF80")) > Error in plot.new() : figure margins too large > In addition: Warning message: > In plotDEXSeq(ecs, geneID = gene, FDR = FDR, lwd = 2, > expression = opts[1], > : > This gene contains more than 42 transcripts annotated, > only the first 42 > will be plotted > > After this error, the function quits and the output is not > complete. Is > there a way to turn this message off and continue outputting > the rest of > the HTML report? > > Thanks, > > sessionInfo() > > R version 2.14.2 (2012-02-29) > Platform: x86_64-apple-darwin9.8.0/x86___64 (64-bit) > > locale: > [1] C/en_US.UTF-8/C/C/C/C > > attached base packages: > [1] grDevices datasets splines graphics utils grid > stats > methods base > > other attached packages: > [1] edgeR_2.4.6 limma_3.10.3 biomaRt_2.10.0 > DEXSeq_1.0.2 > Biobase_2.14.0 plyr_1.7.1 reshape2_1.2.1 > [8] survival_2.36-14 RSQLite_0.11.1 DBI_0.2-5 > knitr_0.5 > gplots_2.10.1 KernSmooth_2.23-7 caTools_1.12 > [15] bitops_1.0-4.1 gdata_2.8.2 gtools_2.6.2 > RColorBrewer_1.0-5 ggplot2_0.9.1 > > loaded via a namespace (and not attached): > [1] MASS_7.3-18 RCurl_1.91-1 Rcpp_0.9.10 > XML_3.9-4 > codetools_0.2-8 colorspace_1.1-1 dichromat_1.2-4 > digest_0.5.2 > [9] evaluate_0.4.2 formatR_0.4 highlight_0.3.1 > hwriter_1.3 > labeling_0.1 memoise_0.1 munsell_0.3 > parser_0.0-14 > [17] proto_0.3-9.2 scales_0.2.1 statmod_1.4.14 > stringr_0.6 > tools_2.14.2 > > > > > > -- > /Ahmet Z./ > > > > > -- > /Ahmet Z./
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