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 â€˜columnsâ€™ for
>> signature â€˜"AffyGenePDInfo"â€™
>>
>
> 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]]

