[BioC] failing to filter ExpressionSet object using nsFilter
James W. MacDonald
jmacdon at uw.edu
Mon Jul 7 02:54:01 CEST 2014
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.
>>>
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>>>
>>
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
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>>
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--
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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