failing to filter ExpressionSet object using nsFilter
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Dear all, I'm trying to use "nsFilter" to filter a post-RMA ExpressionSet (Mouse Gene 2.1), based on low filtering. This object was generated using the "rma" function. However, I get this: > filtered <- nsFilter(myExpressionSet, var.filter=FALSE) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ???columns??? for signature ???"AffyGenePDInfo"??? Any ideas how to troubleshoot this? Thanks, David -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2.db_2.10.1 BiocInstaller_1.12.1 mogene21stprobeset.db_2.13.0 [4] org.Mm.eg.db_2.10.1 VennDiagram_1.6.7 pathview_1.2.4 [7] org.Hs.eg.db_2.10.1 AnnotationDbi_1.24.0 KEGGgraph_1.20.0 [10] graph_1.40.1 XML_3.95-0.2 KEGGREST_1.2.2 [13] pd.mogene.2.1.st_2.12.1 RSQLite_0.11.4 DBI_0.2-7 [16] limma_3.18.13 oligo_1.26.6 Biostrings_2.30.1 [19] XVector_0.2.0 IRanges_1.20.7 oligoClasses_1.24.0 [22] genefilter_1.44.0 affy_1.40.0 Biobase_2.22.0 [25] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affxparser_1.34.2 affyio_1.30.0 annotate_1.40.1 bit_1.1-12 [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 GenomicRanges_1.14.4 [9] httr_0.3 iterators_1.0.7 png_0.1-7 preprocessCore_1.24.0 [13] RCurl_1.95-4.1 Rgraphviz_2.6.0 splines_3.0.2 stats4_3.0.2 [17] stringr_0.6.2 survival_2.37-7 tools_3.0.2 xtable_1.7-3 [21] zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
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Hi David -- On 07/05/2014 05:49 AM, David [guest] wrote: > Dear all, > > I'm trying to use "nsFilter" to filter a post-RMA ExpressionSet (Mouse Gene 2.1), based on low filtering. This object was generated using the "rma" function. However, I get this: > >> filtered <- nsFilter(myExpressionSet, var.filter=FALSE) > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ???columns??? for signature ???"AffyGenePDInfo"??? This is likely a version mismatch between the annotation package per se (pd.*) and the AnnotationDbi package. BiocInstaller::biocValid() might suggest packages that are either too old or too new for your installation. Updating to R-3.1 is also an option, which would imply updating all packages to the current Bioconductor release. Martin > > > Any ideas how to troubleshoot this? > > Thanks, > David > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu95av2.db_2.10.1 BiocInstaller_1.12.1 mogene21stprobeset.db_2.13.0 > [4] org.Mm.eg.db_2.10.1 VennDiagram_1.6.7 pathview_1.2.4 > [7] org.Hs.eg.db_2.10.1 AnnotationDbi_1.24.0 KEGGgraph_1.20.0 > [10] graph_1.40.1 XML_3.95-0.2 KEGGREST_1.2.2 > [13] pd.mogene.2.1.st_2.12.1 RSQLite_0.11.4 DBI_0.2-7 > [16] limma_3.18.13 oligo_1.26.6 Biostrings_2.30.1 > [19] XVector_0.2.0 IRanges_1.20.7 oligoClasses_1.24.0 > [22] genefilter_1.44.0 affy_1.40.0 Biobase_2.22.0 > [25] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.34.2 affyio_1.30.0 annotate_1.40.1 bit_1.1-12 > [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 GenomicRanges_1.14.4 > [9] httr_0.3 iterators_1.0.7 png_0.1-7 preprocessCore_1.24.0 > [13] RCurl_1.95-4.1 Rgraphviz_2.6.0 splines_3.0.2 stats4_3.0.2 > [17] stringr_0.6.2 survival_2.37-7 tools_3.0.2 xtable_1.7-3 > [21] zlibbioc_1.8.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Hi Martin, Thanks for replying. I removed everything and reinstalled R 3.1 and Bioconductor, but still got the same error message. SessionInfo: R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin13.1.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] VennDiagram_1.6.5 pathview_1.4.1 org.Hs.eg.db_2.14.0 AnnotationDbi_1.26.0 [5] GenomeInfoDb_1.0.2 KEGGgraph_1.22.1 graph_1.42.0 XML_3.98-1.1 [9] KEGGREST_1.4.0 pd.mogene.2.1.st_2.14.0 RSQLite_0.11.4 DBI_0.2-7 [13] limma_3.20.8 oligo_1.28.2 Biostrings_2.32.1 XVector_0.4.0 [17] IRanges_1.22.9 oligoClasses_1.26.0 genefilter_1.46.1 affy_1.42.3 [21] Biobase_2.24.0 BiocGenerics_0.10.0 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] affxparser_1.36.0 affyio_1.32.0 annotate_1.42.0 bit_1.1-12 [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 GenomicRanges_1.16.3 [9] httr_0.3 iterators_1.0.7 png_0.1-7 preprocessCore_1.26.1 [13] RCurl_1.95-4.1 Rgraphviz_2.8.1 splines_3.1.0 stats4_3.1.0 [17] stringr_0.6.2 survival_2.37-7 tools_3.1.0 xtable_1.7-3 [21] zlibbioc_1.10.0 On Sat, Jul 5, 2014 at 9:38 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > Hi David -- > > On 07/05/2014 05:49 AM, David [guest] wrote: > >> Dear all, >> >> I'm trying to use "nsFilter" to filter a post-RMA ExpressionSet (Mouse >> Gene 2.1), based on low filtering. This object was generated using the >> "rma" function. However, I get this: >> >> filtered <- nsFilter(myExpressionSet, var.filter=FALSE) >>> >> Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function ‘columns’ for >> signature ‘"AffyGenePDInfo"’ >> > > This is likely a version mismatch between the annotation package per se > (pd.*) and the AnnotationDbi package. > > BiocInstaller::biocValid() > > might suggest packages that are either too old or too new for your > installation. > > Updating to R-3.1 is also an option, which would imply updating all > packages to the current Bioconductor release. > > Martin > > >> >> Any ideas how to troubleshoot this? >> >> Thanks, >> David >> >> -- output of sessionInfo(): >> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] grid parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] hgu95av2.db_2.10.1 BiocInstaller_1.12.1 >> mogene21stprobeset.db_2.13.0 >> [4] org.Mm.eg.db_2.10.1 VennDiagram_1.6.7 >> pathview_1.2.4 >> [7] org.Hs.eg.db_2.10.1 AnnotationDbi_1.24.0 >> KEGGgraph_1.20.0 >> [10] graph_1.40.1 XML_3.95-0.2 >> KEGGREST_1.2.2 >> [13] pd.mogene.2.1.st_2.12.1 RSQLite_0.11.4 DBI_0.2-7 >> [16] limma_3.18.13 oligo_1.26.6 >> Biostrings_2.30.1 >> [19] XVector_0.2.0 IRanges_1.20.7 >> oligoClasses_1.24.0 >> [22] genefilter_1.44.0 affy_1.40.0 >> Biobase_2.22.0 >> [25] BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.34.2 affyio_1.30.0 annotate_1.40.1 >> bit_1.1-12 >> [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 >> GenomicRanges_1.14.4 >> [9] httr_0.3 iterators_1.0.7 png_0.1-7 >> preprocessCore_1.24.0 >> [13] RCurl_1.95-4.1 Rgraphviz_2.6.0 splines_3.0.2 >> stats4_3.0.2 >> [17] stringr_0.6.2 survival_2.37-7 tools_3.0.2 >> xtable_1.7-3 >> [21] zlibbioc_1.8.0 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]
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Dear David I am not the author of that function, but I presume they would need a reproducible code example and or dataset that lets them reproduce the error message that you get and inspect ?myExpressionSet?. Kind regards Wolfgang Wolfgang Huber Principal Investigator, EMBL Senior Scientist Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg, Germany T +49-6221-3878823 wolfgang.huber at embl.de http://www.embl.de/research/units/genome_biology/huber On 6 Jul 2014, at 01:15, David Bomze <bomzed at="" student.ethz.ch=""> wrote: > Hi Martin, > > Thanks for replying. > > I removed everything and reinstalled R 3.1 and Bioconductor, but still got > the same error message. > > > > SessionInfo: > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin13.1.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] VennDiagram_1.6.5 pathview_1.4.1 org.Hs.eg.db_2.14.0 > AnnotationDbi_1.26.0 > [5] GenomeInfoDb_1.0.2 KEGGgraph_1.22.1 graph_1.42.0 > XML_3.98-1.1 > [9] KEGGREST_1.4.0 pd.mogene.2.1.st_2.14.0 RSQLite_0.11.4 > DBI_0.2-7 > [13] limma_3.20.8 oligo_1.28.2 Biostrings_2.32.1 > XVector_0.4.0 > [17] IRanges_1.22.9 oligoClasses_1.26.0 genefilter_1.46.1 > affy_1.42.3 > [21] Biobase_2.24.0 BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] affxparser_1.36.0 affyio_1.32.0 annotate_1.42.0 > bit_1.1-12 > [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 > GenomicRanges_1.16.3 > [9] httr_0.3 iterators_1.0.7 png_0.1-7 > preprocessCore_1.26.1 > [13] RCurl_1.95-4.1 Rgraphviz_2.8.1 splines_3.1.0 > stats4_3.1.0 > [17] stringr_0.6.2 survival_2.37-7 tools_3.1.0 > xtable_1.7-3 > [21] zlibbioc_1.10.0 > > > On Sat, Jul 5, 2014 at 9:38 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > >> Hi David -- >> >> On 07/05/2014 05:49 AM, David [guest] wrote: >> >>> Dear all, >>> >>> I'm trying to use "nsFilter" to filter a post-RMA ExpressionSet (Mouse >>> Gene 2.1), based on low filtering. This object was generated using the >>> "rma" function. However, I get this: >>> >>> filtered <- nsFilter(myExpressionSet, var.filter=FALSE) >>>> >>> Error in (function (classes, fdef, mtable) : >>> unable to find an inherited method for function ???columns??? for >>> signature ???"AffyGenePDInfo"??? >>> >> >> This is likely a version mismatch between the annotation package per se >> (pd.*) and the AnnotationDbi package. >> >> BiocInstaller::biocValid() >> >> might suggest packages that are either too old or too new for your >> installation. >> >> Updating to R-3.1 is also an option, which would imply updating all >> packages to the current Bioconductor release. >> >> Martin >> >> >>> >>> Any ideas how to troubleshoot this? >>> >>> Thanks, >>> David >>> >>> -- output of sessionInfo(): >>> >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] grid parallel stats graphics grDevices utils datasets >>> methods base >>> >>> other attached packages: >>> [1] hgu95av2.db_2.10.1 BiocInstaller_1.12.1 >>> mogene21stprobeset.db_2.13.0 >>> [4] org.Mm.eg.db_2.10.1 VennDiagram_1.6.7 >>> pathview_1.2.4 >>> [7] org.Hs.eg.db_2.10.1 AnnotationDbi_1.24.0 >>> KEGGgraph_1.20.0 >>> [10] graph_1.40.1 XML_3.95-0.2 >>> KEGGREST_1.2.2 >>> [13] pd.mogene.2.1.st_2.12.1 RSQLite_0.11.4 DBI_0.2-7 >>> [16] limma_3.18.13 oligo_1.26.6 >>> Biostrings_2.30.1 >>> [19] XVector_0.2.0 IRanges_1.20.7 >>> oligoClasses_1.24.0 >>> [22] genefilter_1.44.0 affy_1.40.0 >>> Biobase_2.22.0 >>> [25] BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.34.2 affyio_1.30.0 annotate_1.40.1 >>> bit_1.1-12 >>> [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 >>> GenomicRanges_1.14.4 >>> [9] httr_0.3 iterators_1.0.7 png_0.1-7 >>> preprocessCore_1.24.0 >>> [13] RCurl_1.95-4.1 Rgraphviz_2.6.0 splines_3.0.2 >>> stats4_3.0.2 >>> [17] stringr_0.6.2 survival_2.37-7 tools_3.0.2 >>> xtable_1.7-3 >>> [21] zlibbioc_1.8.0 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> 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 >>> >>> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 >> > > [[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 David, The problem is due to the fact that the annotation for your ExpressionSet is by default 'pd.mogene.2.1.st', which is the database used for mapping probes to probesets, not probesets to annotation. In order to use things like nsFilter, you need to 'swap' the annotation. Assuming you just used rma() without changing the target argument, then you want to do this: annotation(myExpressionSet) <- "mogene21sttranscriptcluster.db" and then you should be able to proceed without further problems. If you used target = "probe", which I would caution against doing, then you need to do annotation(myExpressionSet) <- "mogene21stprobeset.db" Best, Jim On 7/5/2014 7:15 PM, David Bomze wrote: > Hi Martin, > > Thanks for replying. > > I removed everything and reinstalled R 3.1 and Bioconductor, but still got > the same error message. > > > > SessionInfo: > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin13.1.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] VennDiagram_1.6.5 pathview_1.4.1 org.Hs.eg.db_2.14.0 > AnnotationDbi_1.26.0 > [5] GenomeInfoDb_1.0.2 KEGGgraph_1.22.1 graph_1.42.0 > XML_3.98-1.1 > [9] KEGGREST_1.4.0 pd.mogene.2.1.st_2.14.0 RSQLite_0.11.4 > DBI_0.2-7 > [13] limma_3.20.8 oligo_1.28.2 Biostrings_2.32.1 > XVector_0.4.0 > [17] IRanges_1.22.9 oligoClasses_1.26.0 genefilter_1.46.1 > affy_1.42.3 > [21] Biobase_2.24.0 BiocGenerics_0.10.0 BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] affxparser_1.36.0 affyio_1.32.0 annotate_1.42.0 > bit_1.1-12 > [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 > GenomicRanges_1.16.3 > [9] httr_0.3 iterators_1.0.7 png_0.1-7 > preprocessCore_1.26.1 > [13] RCurl_1.95-4.1 Rgraphviz_2.8.1 splines_3.1.0 > stats4_3.1.0 > [17] stringr_0.6.2 survival_2.37-7 tools_3.1.0 > xtable_1.7-3 > [21] zlibbioc_1.10.0 > > > On Sat, Jul 5, 2014 at 9:38 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > >> Hi David -- >> >> On 07/05/2014 05:49 AM, David [guest] wrote: >> >>> Dear all, >>> >>> I'm trying to use "nsFilter" to filter a post-RMA ExpressionSet (Mouse >>> Gene 2.1), based on low filtering. This object was generated using the >>> "rma" function. However, I get this: >>> >>> filtered <- nsFilter(myExpressionSet, var.filter=FALSE) >>>> >>> Error in (function (classes, fdef, mtable) : >>> unable to find an inherited method for function ???????columns???????? for >>> signature ???????"AffyGenePDInfo"???????? >>> >> >> This is likely a version mismatch between the annotation package per se >> (pd.*) and the AnnotationDbi package. >> >> BiocInstaller::biocValid() >> >> might suggest packages that are either too old or too new for your >> installation. >> >> Updating to R-3.1 is also an option, which would imply updating all >> packages to the current Bioconductor release. >> >> Martin >> >> >>> >>> Any ideas how to troubleshoot this? >>> >>> Thanks, >>> David >>> >>> -- output of sessionInfo(): >>> >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] grid parallel stats graphics grDevices utils datasets >>> methods base >>> >>> other attached packages: >>> [1] hgu95av2.db_2.10.1 BiocInstaller_1.12.1 >>> mogene21stprobeset.db_2.13.0 >>> [4] org.Mm.eg.db_2.10.1 VennDiagram_1.6.7 >>> pathview_1.2.4 >>> [7] org.Hs.eg.db_2.10.1 AnnotationDbi_1.24.0 >>> KEGGgraph_1.20.0 >>> [10] graph_1.40.1 XML_3.95-0.2 >>> KEGGREST_1.2.2 >>> [13] pd.mogene.2.1.st_2.12.1 RSQLite_0.11.4 DBI_0.2-7 >>> [16] limma_3.18.13 oligo_1.26.6 >>> Biostrings_2.30.1 >>> [19] XVector_0.2.0 IRanges_1.20.7 >>> oligoClasses_1.24.0 >>> [22] genefilter_1.44.0 affy_1.40.0 >>> Biobase_2.22.0 >>> [25] BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.34.2 affyio_1.30.0 annotate_1.40.1 >>> bit_1.1-12 >>> [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 >>> GenomicRanges_1.14.4 >>> [9] httr_0.3 iterators_1.0.7 png_0.1-7 >>> preprocessCore_1.24.0 >>> [13] RCurl_1.95-4.1 Rgraphviz_2.6.0 splines_3.0.2 >>> stats4_3.0.2 >>> [17] stringr_0.6.2 survival_2.37-7 tools_3.0.2 >>> xtable_1.7-3 >>> [21] zlibbioc_1.8.0 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> 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 >>> >>> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 >> > > [[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 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi Jim, Works like a charm. Many thanks, David On Mon, Jul 7, 2014 at 2:54 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi David, > > The problem is due to the fact that the annotation for your ExpressionSet > is by default 'pd.mogene.2.1.st', which is the database used for mapping > probes to probesets, not probesets to annotation. > > In order to use things like nsFilter, you need to 'swap' the annotation. > Assuming you just used rma() without changing the target argument, then you > want to do this: > > annotation(myExpressionSet) <- "mogene21sttranscriptcluster.db" > > and then you should be able to proceed without further problems. If you > used target = "probe", which I would caution against doing, then you need > to do > > annotation(myExpressionSet) <- "mogene21stprobeset.db" > > Best, > > Jim > > > > On 7/5/2014 7:15 PM, David Bomze wrote: > >> Hi Martin, >> >> Thanks for replying. >> >> I removed everything and reinstalled R 3.1 and Bioconductor, but still got >> the same error message. >> >> >> >> SessionInfo: >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-apple-darwin13.1.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] grid parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] VennDiagram_1.6.5 pathview_1.4.1 org.Hs.eg.db_2.14.0 >> AnnotationDbi_1.26.0 >> [5] GenomeInfoDb_1.0.2 KEGGgraph_1.22.1 graph_1.42.0 >> XML_3.98-1.1 >> [9] KEGGREST_1.4.0 pd.mogene.2.1.st_2.14.0 RSQLite_0.11.4 >> DBI_0.2-7 >> [13] limma_3.20.8 oligo_1.28.2 Biostrings_2.32.1 >> XVector_0.4.0 >> [17] IRanges_1.22.9 oligoClasses_1.26.0 genefilter_1.46.1 >> affy_1.42.3 >> [21] Biobase_2.24.0 BiocGenerics_0.10.0 BiocInstaller_1.14.2 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.36.0 affyio_1.32.0 annotate_1.42.0 >> bit_1.1-12 >> [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 >> GenomicRanges_1.16.3 >> [9] httr_0.3 iterators_1.0.7 png_0.1-7 >> preprocessCore_1.26.1 >> [13] RCurl_1.95-4.1 Rgraphviz_2.8.1 splines_3.1.0 >> stats4_3.1.0 >> [17] stringr_0.6.2 survival_2.37-7 tools_3.1.0 >> xtable_1.7-3 >> [21] zlibbioc_1.10.0 >> >> >> On Sat, Jul 5, 2014 at 9:38 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: >> >> Hi David -- >>> >>> On 07/05/2014 05:49 AM, David [guest] wrote: >>> >>> Dear all, >>>> >>>> I'm trying to use "nsFilter" to filter a post-RMA ExpressionSet (Mouse >>>> Gene 2.1), based on low filtering. This object was generated using the >>>> "rma" function. However, I get this: >>>> >>>> filtered <- nsFilter(myExpressionSet, var.filter=FALSE) >>>> >>>>> >>>>> Error in (function (classes, fdef, mtable) : >>>> unable to find an inherited method for function >>>> ‘columns’ for >>>> signature ‘"AffyGenePDInfo"’ >>>> >>>> >>> This is likely a version mismatch between the annotation package per se >>> (pd.*) and the AnnotationDbi package. >>> >>> BiocInstaller::biocValid() >>> >>> might suggest packages that are either too old or too new for your >>> installation. >>> >>> Updating to R-3.1 is also an option, which would imply updating all >>> packages to the current Bioconductor release. >>> >>> Martin >>> >>> >>> >>>> Any ideas how to troubleshoot this? >>>> >>>> Thanks, >>>> David >>>> >>>> -- output of sessionInfo(): >>>> >>>> R version 3.0.2 (2013-09-25) >>>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>>> >>>> locale: >>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>>> >>>> attached base packages: >>>> [1] grid parallel stats graphics grDevices utils datasets >>>> methods base >>>> >>>> other attached packages: >>>> [1] hgu95av2.db_2.10.1 BiocInstaller_1.12.1 >>>> mogene21stprobeset.db_2.13.0 >>>> [4] org.Mm.eg.db_2.10.1 VennDiagram_1.6.7 >>>> pathview_1.2.4 >>>> [7] org.Hs.eg.db_2.10.1 AnnotationDbi_1.24.0 >>>> KEGGgraph_1.20.0 >>>> [10] graph_1.40.1 XML_3.95-0.2 >>>> KEGGREST_1.2.2 >>>> [13] pd.mogene.2.1.st_2.12.1 RSQLite_0.11.4 DBI_0.2-7 >>>> [16] limma_3.18.13 oligo_1.26.6 >>>> Biostrings_2.30.1 >>>> [19] XVector_0.2.0 IRanges_1.20.7 >>>> oligoClasses_1.24.0 >>>> [22] genefilter_1.44.0 affy_1.40.0 >>>> Biobase_2.22.0 >>>> [25] BiocGenerics_0.8.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affxparser_1.34.2 affyio_1.30.0 annotate_1.40.1 >>>> bit_1.1-12 >>>> [5] codetools_0.2-8 ff_2.2-13 foreach_1.4.2 >>>> GenomicRanges_1.14.4 >>>> [9] httr_0.3 iterators_1.0.7 png_0.1-7 >>>> preprocessCore_1.24.0 >>>> [13] RCurl_1.95-4.1 Rgraphviz_2.6.0 splines_3.0.2 >>>> stats4_3.0.2 >>>> [17] stringr_0.6.2 survival_2.37-7 tools_3.0.2 >>>> xtable_1.7-3 >>>> [21] zlibbioc_1.8.0 >>>> >>>> -- >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane. >>>> science.biology.informatics.conductor >>>> >>>> >>>> >>> -- >>> Computational Biology / Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. >>> PO Box 19024 Seattle, WA 98109 >>> >>> Location: Arnold Building M1 B861 >>> Phone: (206) 667-2793 >>> >>> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > [[alternative HTML version deleted]]
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