[BioC] failing to filter ExpressionSet object using nsFilter

Wolfgang Huber whuber at embl.de
Sun Jul 6 17:42:40 CEST 2014


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.
>>> 
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>>> 
>> 
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
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>> 
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>> 
> 
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