[BioC] failing to filter ExpressionSet object using nsFilter

[David [guest]]

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"’


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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