[BioC] qc in simpleaffy

[Martin Morgan]

Hi Mayte --

Mayte Suarez-Farinas <farinam at mail.rockefeller.edu> writes:

> Hi everybody:
>
> I am working with R 2.8 and I the function "qc" from simpleaffy is
> not working:
>
>  > q<-qc(abatch)
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "annotation", for
>    signature "AffyBatch"

I think IRanges::annotation is masking Biobase::annotation. This might
be solved by updating packages, specifically IRanges. Have you tried
updating your packages

  http://bioconductor.org/docs/install/

? From the prompt I think Biobase::annotation(abatch) will work, and
that

  annotation <- Biobase::annotation
  qc(abatch)

will too. And that R 2.9 / Bioc 2.4will also avoid this problem.

Martin

> I get the same error if:
>
>  >annotation(abatch)
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "annotation", for
>    signature "AffyBatch"
>
> but not if:
>
>  > abatch at annotation
> [1] "hgu133a2.db"
>
>
> sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils
> datasets  methods   base
>
> other attached packages:
>   [1] hgu133plus2probe_2.3.0 hgu133plus2cdf_2.3.0    Harshlight_1.12.0
>   altcdfenvs_2.4.0
>   [5] hypergraph_1.14.0      Biostrings_2.10.16      IRanges_1.0.12
>   makecdfenv_1.20.0
>   [9] affyio_1.10.1          beadarray_1.10.0        sma_0.5.15
>   hwriter_1.0
> [13] affycoretools_1.14.1   annaffy_1.14.0          KEGG.db_2.2.5
> biomaRt_1.16.0
> [17] GOstats_2.8.0          Category_2.8.4          RBGL_1.18.0
> GO.db_2.2.5
> [21] RSQLite_0.7-1          DBI_0.2-4               graph_1.20.0
> limma_2.16.4
> [25] affyQCReport_1.20.0    geneplotter_1.20.0      annotate_1.20.1
> AnnotationDbi_1.5.18
> [29] lattice_0.17-17        RColorBrewer_1.0-2      affyPLM_1.18.1
> preprocessCore_1.4.0
> [33] xtable_1.5-4           simpleaffy_2.18.0       gcrma_2.14.1
> matchprobes_1.14.1
> [37] genefilter_1.22.0      survival_2.34-1         affy_1.20.2
> Biobase_2.2.2
>
> loaded via a namespace (and not attached):
> [1] GSEABase_1.4.0     KernSmooth_2.22-22 Matrix_0.999375-21
> RCurl_0.94-1       XML_2.1-0
> [6] cluster_1.11.11    grid_2.8.1
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793