[BioC] failing to filter ExpressionSet object using nsFilter

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 Ã¢â‚¬ËœcolumnsÃ¢â‚¬â„¢ for
>>> signature Ã¢â‚¬Ëœ"AffyGenePDInfo"Ã¢â‚¬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
>>>
>>> --
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>>>
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>>>
>>
>> --
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>>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099