svg error in arrayQualityMetrics
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@straubhaar-juerg-391
Last seen 10.2 years ago
I am running the arrayQualityMetrics with: arrayQualityMetrics(expressionset=esett,outdir="TestAQM",force=TRUE,do .logtransform=FALSE,intgroup="SomeCategory") and get the following errror: Error in tmp[i] : invalid subscript type 'list' The error is generated in a 'brittle' part of the arrayQualityMetrics code on line 31 of the annotateSvgMapPlot.R source file, in the function annotateSvgPlot(). Line 31 of this file is prepended with a comment pointing to the 'brittle' nature of this part of the code and says '...getPlotObjNodes' will be 'getMatplotSeries' or 'getPlotPoints' from ## 'SVGAnnotation', which rely on conventions used by libcairo ... I replaced getPlotObjNodes in annotateSvgPlot() with getMatplotSeries() and getPlotPoints() to no avail. > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] C attached base packages: [1] grDevices datasets parallel stats graphics utils methods [8] base other attached packages: [1] arrayQualityMetrics_3.18.0 AnnotationDbi_1.24.0 [3] Biobase_2.22.0 BiocGenerics_0.8.0 [5] RSQLite_0.11.4 DBI_0.2-7 loaded via a namespace (and not attached): [1] AnnotationForge_1.4.4 BSgenome_1.30.0 BeadDataPackR_1.14.0 [4] BiocInstaller_1.12.0 Biostrings_2.30.1 Cairo_1.5-5 [7] Category_2.28.0 DESeq2_1.2.10 DO.db_2.7 [10] DOSE_2.0.0 Formula_1.1-1 GO.db_2.10.1 [13] GOSemSim_1.20.3 GOstats_2.28.0 GSEABase_1.24.0 [16] GenomicFeatures_1.14.3 GenomicRanges_1.14.4 Hmisc_3.14-3 [19] IRanges_1.20.7 KEGG.db_2.10.1 KernSmooth_2.23-10 [22] MASS_7.3-29 Matrix_1.1-2-2 PFAM.db_2.10.1 [25] R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.29.8 [28] RBGL_1.38.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 [31] Rcpp_0.11.0 RcppArmadillo_0.4.100.0 ReportingTools_2.2.0 [34] Rsamtools_1.14.3 SVGAnnotation_0.93-1 VariantAnnotation_1.8.12 [37] XML_3.98-1.1 XVector_0.2.0 affy_1.40.0 [40] affyPLM_1.38.0 affyio_1.30.0 annotate_1.40.1 [43] beadarray_2.12.0 biomaRt_2.18.0 biovizBase_1.10.8 [46] bitops_1.0-6 cluster_1.14.4 clusterProfiler_1.10.1 [49] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 [52] edgeR_3.4.2 gcrma_2.34.0 genefilter_1.44.0 [55] ggbio_1.10.12 ggplot2_0.9.3.1 graph_1.40.1 [58] grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2 [61] hwriter_1.3 igraph_0.7.0 labeling_0.2 [64] lattice_0.20-27 latticeExtra_0.6-26 limma_3.18.13 [67] locfit_1.5-9.1 munsell_0.4.2 plyr_1.8.1 [70] preprocessCore_1.24.0 proto_0.3-10 qvalue_1.36.0 [73] reshape2_1.2.2 rtracklayer_1.22.4 scales_0.2.3 [76] setRNG_2011.11-2 splines_3.0.2 stats4_3.0.2 [79] stringr_0.6.2 survival_2.37-7 tcltk_3.0.2 [82] tools_3.0.2 vsn_3.30.0 xtable_1.7-1 [85] zlibbioc_1.8.0 Thank you. Juerg Straubhaar University of Massachusetts Medical School
GO arrayQualityMetrics GO arrayQualityMetrics • 1.5k views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear Juerg what do you get from $ pkg-config --modversion cairo E.g. on my system I get 1.12.16. Also, please try with the current devel version of the package: http:/ /www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics.htm l Only if all that fails it seems worthwhile to descend into code debugging. Kind regards Wolfgang Il giorno 07 Mar 2014, alle ore 19:17, Straubhaar, Juerg <juerg.straubhaar at="" umassmed.edu=""> ha scritto: > I am running the arrayQualityMetrics with: > > arrayQualityMetrics(expressionset=esett,outdir="TestAQM",force=TRUE, do.logtransform=FALSE,intgroup="SomeCategory") > > and get the following errror: > > Error in tmp[i] : invalid subscript type 'list' > > The error is generated in a 'brittle' part of the arrayQualityMetrics code on line 31 of the annotateSvgMapPlot.R source file, in the function annotateSvgPlot(). > Line 31 of this file is prepended with a comment pointing to the 'brittle' nature of this part of the code and says > > '...getPlotObjNodes' will be 'getMatplotSeries' or 'getPlotPoints' from > ## 'SVGAnnotation', which rely on conventions used by libcairo ... > > I replaced getPlotObjNodes in annotateSvgPlot() with getMatplotSeries() and getPlotPoints() to no avail. > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] grDevices datasets parallel stats graphics utils methods > [8] base > > other attached packages: > [1] arrayQualityMetrics_3.18.0 AnnotationDbi_1.24.0 > [3] Biobase_2.22.0 BiocGenerics_0.8.0 > [5] RSQLite_0.11.4 DBI_0.2-7 > > loaded via a namespace (and not attached): > [1] AnnotationForge_1.4.4 BSgenome_1.30.0 BeadDataPackR_1.14.0 > [4] BiocInstaller_1.12.0 Biostrings_2.30.1 Cairo_1.5-5 > [7] Category_2.28.0 DESeq2_1.2.10 DO.db_2.7 > [10] DOSE_2.0.0 Formula_1.1-1 GO.db_2.10.1 > [13] GOSemSim_1.20.3 GOstats_2.28.0 GSEABase_1.24.0 > [16] GenomicFeatures_1.14.3 GenomicRanges_1.14.4 Hmisc_3.14-3 > [19] IRanges_1.20.7 KEGG.db_2.10.1 KernSmooth_2.23-10 > [22] MASS_7.3-29 Matrix_1.1-2-2 PFAM.db_2.10.1 > [25] R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.29.8 > [28] RBGL_1.38.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 > [31] Rcpp_0.11.0 RcppArmadillo_0.4.100.0 ReportingTools_2.2.0 > [34] Rsamtools_1.14.3 SVGAnnotation_0.93-1 VariantAnnotation_1.8.12 > [37] XML_3.98-1.1 XVector_0.2.0 affy_1.40.0 > [40] affyPLM_1.38.0 affyio_1.30.0 annotate_1.40.1 > [43] beadarray_2.12.0 biomaRt_2.18.0 biovizBase_1.10.8 > [46] bitops_1.0-6 cluster_1.14.4 clusterProfiler_1.10.1 > [49] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 > [52] edgeR_3.4.2 gcrma_2.34.0 genefilter_1.44.0 > [55] ggbio_1.10.12 ggplot2_0.9.3.1 graph_1.40.1 > [58] grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2 > [61] hwriter_1.3 igraph_0.7.0 labeling_0.2 > [64] lattice_0.20-27 latticeExtra_0.6-26 limma_3.18.13 > [67] locfit_1.5-9.1 munsell_0.4.2 plyr_1.8.1 > [70] preprocessCore_1.24.0 proto_0.3-10 qvalue_1.36.0 > [73] reshape2_1.2.2 rtracklayer_1.22.4 scales_0.2.3 > [76] setRNG_2011.11-2 splines_3.0.2 stats4_3.0.2 > [79] stringr_0.6.2 survival_2.37-7 tcltk_3.0.2 > [82] tools_3.0.2 vsn_3.30.0 xtable_1.7-1 > [85] zlibbioc_1.8.0 > > Thank you. > > Juerg Straubhaar > University of Massachusetts Medical School > _______________________________________________ > 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 Wolfgang, My cairo version is 1.12.14 and I didn't like to update to your version since for gentoo linux version 1.12.16 is still unstable. But I used arrayQualityMetrics devel version and it worked with cairo version 1.12.14. I apologize for bothering you. I should have thought about testing the devel package version before using the list. Thank you. Juerg ________________________________________ From: Wolfgang Huber [whuber@embl.de] Sent: Sunday, March 09, 2014 6:18 PM To: Straubhaar, Juerg Cc: bioconductor at r-project.org Subject: Re: [BioC] svg error in arrayQualityMetrics Dear Juerg what do you get from $ pkg-config --modversion cairo E.g. on my system I get 1.12.16. Also, please try with the current devel version of the package: http:/ /www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics.htm l Only if all that fails it seems worthwhile to descend into code debugging. Kind regards Wolfgang Il giorno 07 Mar 2014, alle ore 19:17, Straubhaar, Juerg <juerg.straubhaar at="" umassmed.edu=""> ha scritto: > I am running the arrayQualityMetrics with: > > arrayQualityMetrics(expressionset=esett,outdir="TestAQM",force=TRUE, do.logtransform=FALSE,intgroup="SomeCategory") > > and get the following errror: > > Error in tmp[i] : invalid subscript type 'list' > > The error is generated in a 'brittle' part of the arrayQualityMetrics code on line 31 of the annotateSvgMapPlot.R source file, in the function annotateSvgPlot(). > Line 31 of this file is prepended with a comment pointing to the 'brittle' nature of this part of the code and says > > '...getPlotObjNodes' will be 'getMatplotSeries' or 'getPlotPoints' from > ## 'SVGAnnotation', which rely on conventions used by libcairo ... > > I replaced getPlotObjNodes in annotateSvgPlot() with getMatplotSeries() and getPlotPoints() to no avail. > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] grDevices datasets parallel stats graphics utils methods > [8] base > > other attached packages: > [1] arrayQualityMetrics_3.18.0 AnnotationDbi_1.24.0 > [3] Biobase_2.22.0 BiocGenerics_0.8.0 > [5] RSQLite_0.11.4 DBI_0.2-7 > > loaded via a namespace (and not attached): > [1] AnnotationForge_1.4.4 BSgenome_1.30.0 BeadDataPackR_1.14.0 > [4] BiocInstaller_1.12.0 Biostrings_2.30.1 Cairo_1.5-5 > [7] Category_2.28.0 DESeq2_1.2.10 DO.db_2.7 > [10] DOSE_2.0.0 Formula_1.1-1 GO.db_2.10.1 > [13] GOSemSim_1.20.3 GOstats_2.28.0 GSEABase_1.24.0 > [16] GenomicFeatures_1.14.3 GenomicRanges_1.14.4 Hmisc_3.14-3 > [19] IRanges_1.20.7 KEGG.db_2.10.1 KernSmooth_2.23-10 > [22] MASS_7.3-29 Matrix_1.1-2-2 PFAM.db_2.10.1 > [25] R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.29.8 > [28] RBGL_1.38.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 > [31] Rcpp_0.11.0 RcppArmadillo_0.4.100.0 ReportingTools_2.2.0 > [34] Rsamtools_1.14.3 SVGAnnotation_0.93-1 VariantAnnotation_1.8.12 > [37] XML_3.98-1.1 XVector_0.2.0 affy_1.40.0 > [40] affyPLM_1.38.0 affyio_1.30.0 annotate_1.40.1 > [43] beadarray_2.12.0 biomaRt_2.18.0 biovizBase_1.10.8 > [46] bitops_1.0-6 cluster_1.14.4 clusterProfiler_1.10.1 > [49] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 > [52] edgeR_3.4.2 gcrma_2.34.0 genefilter_1.44.0 > [55] ggbio_1.10.12 ggplot2_0.9.3.1 graph_1.40.1 > [58] grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2 > [61] hwriter_1.3 igraph_0.7.0 labeling_0.2 > [64] lattice_0.20-27 latticeExtra_0.6-26 limma_3.18.13 > [67] locfit_1.5-9.1 munsell_0.4.2 plyr_1.8.1 > [70] preprocessCore_1.24.0 proto_0.3-10 qvalue_1.36.0 > [73] reshape2_1.2.2 rtracklayer_1.22.4 scales_0.2.3 > [76] setRNG_2011.11-2 splines_3.0.2 stats4_3.0.2 > [79] stringr_0.6.2 survival_2.37-7 tcltk_3.0.2 > [82] tools_3.0.2 vsn_3.30.0 xtable_1.7-1 > [85] zlibbioc_1.8.0 > > Thank you. > > Juerg Straubhaar > University of Massachusetts Medical School > _______________________________________________ > 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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Il giorno 10 Mar 2014, alle ore 14:59, Straubhaar, Juerg <juerg.straubhaar at="" umassmed.edu=""> ha scritto: > Hi Wolfgang, > > My cairo version is 1.12.14 and I didn't like to update to your version since for gentoo linux version 1.12.16 is still unstable. > > But I used arrayQualityMetrics devel version and it worked with cairo version 1.12.14. > > I apologize for bothering you. I should have thought about testing the devel package version before using the list. > Hi Juerg no problem. These things are complex. Anyway, as a general principle, it is true, before reporting a bug or a problem, it is good to try with the latest version in devel. For many we things we find, we find that others have found them before. Wolfgang > Thank you. > > Juerg > ________________________________________ > From: Wolfgang Huber [whuber at embl.de] > Sent: Sunday, March 09, 2014 6:18 PM > To: Straubhaar, Juerg > Cc: bioconductor at r-project.org > Subject: Re: [BioC] svg error in arrayQualityMetrics > > Dear Juerg > > what do you get from > $ pkg-config --modversion cairo > > E.g. on my system I get 1.12.16. > > Also, please try with the current devel version of the package: http ://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics.h tml > > Only if all that fails it seems worthwhile to descend into code debugging. > > Kind regards > Wolfgang > > > Il giorno 07 Mar 2014, alle ore 19:17, Straubhaar, Juerg <juerg.straubhaar at="" umassmed.edu=""> ha scritto: > >> I am running the arrayQualityMetrics with: >> >> arrayQualityMetrics(expressionset=esett,outdir="TestAQM",force=TRUE ,do.logtransform=FALSE,intgroup="SomeCategory") >> >> and get the following errror: >> >> Error in tmp[i] : invalid subscript type 'list' >> >> The error is generated in a 'brittle' part of the arrayQualityMetrics code on line 31 of the annotateSvgMapPlot.R source file, in the function annotateSvgPlot(). >> Line 31 of this file is prepended with a comment pointing to the 'brittle' nature of this part of the code and says >> >> '...getPlotObjNodes' will be 'getMatplotSeries' or 'getPlotPoints' from >> ## 'SVGAnnotation', which rely on conventions used by libcairo ... >> >> I replaced getPlotObjNodes in annotateSvgPlot() with getMatplotSeries() and getPlotPoints() to no avail. >> >>> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] grDevices datasets parallel stats graphics utils methods >> [8] base >> >> other attached packages: >> [1] arrayQualityMetrics_3.18.0 AnnotationDbi_1.24.0 >> [3] Biobase_2.22.0 BiocGenerics_0.8.0 >> [5] RSQLite_0.11.4 DBI_0.2-7 >> >> loaded via a namespace (and not attached): >> [1] AnnotationForge_1.4.4 BSgenome_1.30.0 BeadDataPackR_1.14.0 >> [4] BiocInstaller_1.12.0 Biostrings_2.30.1 Cairo_1.5-5 >> [7] Category_2.28.0 DESeq2_1.2.10 DO.db_2.7 >> [10] DOSE_2.0.0 Formula_1.1-1 GO.db_2.10.1 >> [13] GOSemSim_1.20.3 GOstats_2.28.0 GSEABase_1.24.0 >> [16] GenomicFeatures_1.14.3 GenomicRanges_1.14.4 Hmisc_3.14-3 >> [19] IRanges_1.20.7 KEGG.db_2.10.1 KernSmooth_2.23-10 >> [22] MASS_7.3-29 Matrix_1.1-2-2 PFAM.db_2.10.1 >> [25] R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.29.8 >> [28] RBGL_1.38.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> [31] Rcpp_0.11.0 RcppArmadillo_0.4.100.0 ReportingTools_2.2.0 >> [34] Rsamtools_1.14.3 SVGAnnotation_0.93-1 VariantAnnotation_1.8.12 >> [37] XML_3.98-1.1 XVector_0.2.0 affy_1.40.0 >> [40] affyPLM_1.38.0 affyio_1.30.0 annotate_1.40.1 >> [43] beadarray_2.12.0 biomaRt_2.18.0 biovizBase_1.10.8 >> [46] bitops_1.0-6 cluster_1.14.4 clusterProfiler_1.10.1 >> [49] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 >> [52] edgeR_3.4.2 gcrma_2.34.0 genefilter_1.44.0 >> [55] ggbio_1.10.12 ggplot2_0.9.3.1 graph_1.40.1 >> [58] grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2 >> [61] hwriter_1.3 igraph_0.7.0 labeling_0.2 >> [64] lattice_0.20-27 latticeExtra_0.6-26 limma_3.18.13 >> [67] locfit_1.5-9.1 munsell_0.4.2 plyr_1.8.1 >> [70] preprocessCore_1.24.0 proto_0.3-10 qvalue_1.36.0 >> [73] reshape2_1.2.2 rtracklayer_1.22.4 scales_0.2.3 >> [76] setRNG_2011.11-2 splines_3.0.2 stats4_3.0.2 >> [79] stringr_0.6.2 survival_2.37-7 tcltk_3.0.2 >> [82] tools_3.0.2 vsn_3.30.0 xtable_1.7-1 >> [85] zlibbioc_1.8.0 >> >> Thank you. >> >> Juerg Straubhaar >> University of Massachusetts Medical School >> _______________________________________________ >> 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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Andrzej Oleś ▴ 750
@andrzej-oles-5540
Last seen 4.0 years ago
Heidelberg, Germany
Dear Juerg, the error message is most probably due to an incompatibility with the recent Cairo libraries, which has been fixed in the devel version 3.19.2 of 'arrayQualityMetrics'. As already suggested by Wolfgang, please check whether switching to the newest version resolves the issue. Cheers, Andrzej On Fri, Mar 7, 2014 at 7:17 PM, Straubhaar, Juerg <juerg.straubhaar at="" umassmed.edu=""> wrote: > I am running the arrayQualityMetrics with: > > arrayQualityMetrics(expressionset=esett,outdir="TestAQM",force=TRUE, do.logtransform=FALSE,intgroup="SomeCategory") > > and get the following errror: > > Error in tmp[i] : invalid subscript type 'list' > > The error is generated in a 'brittle' part of the arrayQualityMetrics code on line 31 of the annotateSvgMapPlot.R source file, in the function annotateSvgPlot(). > Line 31 of this file is prepended with a comment pointing to the 'brittle' nature of this part of the code and says > > '...getPlotObjNodes' will be 'getMatplotSeries' or 'getPlotPoints' from > ## 'SVGAnnotation', which rely on conventions used by libcairo ... > > I replaced getPlotObjNodes in annotateSvgPlot() with getMatplotSeries() and getPlotPoints() to no avail. > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] grDevices datasets parallel stats graphics utils methods > [8] base > > other attached packages: > [1] arrayQualityMetrics_3.18.0 AnnotationDbi_1.24.0 > [3] Biobase_2.22.0 BiocGenerics_0.8.0 > [5] RSQLite_0.11.4 DBI_0.2-7 > > loaded via a namespace (and not attached): > [1] AnnotationForge_1.4.4 BSgenome_1.30.0 BeadDataPackR_1.14.0 > [4] BiocInstaller_1.12.0 Biostrings_2.30.1 Cairo_1.5-5 > [7] Category_2.28.0 DESeq2_1.2.10 DO.db_2.7 > [10] DOSE_2.0.0 Formula_1.1-1 GO.db_2.10.1 > [13] GOSemSim_1.20.3 GOstats_2.28.0 GSEABase_1.24.0 > [16] GenomicFeatures_1.14.3 GenomicRanges_1.14.4 Hmisc_3.14-3 > [19] IRanges_1.20.7 KEGG.db_2.10.1 KernSmooth_2.23-10 > [22] MASS_7.3-29 Matrix_1.1-2-2 PFAM.db_2.10.1 > [25] R.methodsS3_1.6.1 R.oo_1.18.0 R.utils_1.29.8 > [28] RBGL_1.38.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 > [31] Rcpp_0.11.0 RcppArmadillo_0.4.100.0 ReportingTools_2.2.0 > [34] Rsamtools_1.14.3 SVGAnnotation_0.93-1 VariantAnnotation_1.8.12 > [37] XML_3.98-1.1 XVector_0.2.0 affy_1.40.0 > [40] affyPLM_1.38.0 affyio_1.30.0 annotate_1.40.1 > [43] beadarray_2.12.0 biomaRt_2.18.0 biovizBase_1.10.8 > [46] bitops_1.0-6 cluster_1.14.4 clusterProfiler_1.10.1 > [49] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 > [52] edgeR_3.4.2 gcrma_2.34.0 genefilter_1.44.0 > [55] ggbio_1.10.12 ggplot2_0.9.3.1 graph_1.40.1 > [58] grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2 > [61] hwriter_1.3 igraph_0.7.0 labeling_0.2 > [64] lattice_0.20-27 latticeExtra_0.6-26 limma_3.18.13 > [67] locfit_1.5-9.1 munsell_0.4.2 plyr_1.8.1 > [70] preprocessCore_1.24.0 proto_0.3-10 qvalue_1.36.0 > [73] reshape2_1.2.2 rtracklayer_1.22.4 scales_0.2.3 > [76] setRNG_2011.11-2 splines_3.0.2 stats4_3.0.2 > [79] stringr_0.6.2 survival_2.37-7 tcltk_3.0.2 > [82] tools_3.0.2 vsn_3.30.0 xtable_1.7-1 > [85] zlibbioc_1.8.0 > > Thank you. > > Juerg Straubhaar > University of Massachusetts Medical School > _______________________________________________ > 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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