[BioC] failing to filter ExpressionSet object using nsFilter

[Martin Morgan]

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.
>
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