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]]