[BioC] Human Gene ST using oligo package

[Benilton Carvalho]

detach affy and try again (when you loaded 'affy' you got a message
saying that oligo::probeNames was being masked).

fyi: we do have ideas on how to solve this.

b

2010/5/19 Javier Pérez Florido <jpflorido at gmail.com>:
> Dear list,
> Some time ago I used the oligo package to read and pre-process (rma) a set
> of Human Gene ST 1.0 CEL files and it was OK.
>
> Now, I have resumed my work and with the new version of oligo and R (below
> is my session info), the same code doesn't work (the new oligo vignette is
> quite different to the one I used before). I have downloaded first the
> pd.hugene.1.0.st package from bioconductor and then I built it myself (to
> check if it was a problem of the annotation package) and the same error
> appears:
>
> OligoRaw<-read.celfiles(filenames=list.celfiles())
> OligoEset<-rma(OligoRaw,target="core") # It is a GeneFeatureSet object
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "probeNames", for signature
> "GeneFeatureSet"
>
> Any suggestions?
> Thanks,
> Javier
>
>
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
>  LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
> [5] LC_TIME=Spanish_Spain.1252
>
> attached base packages:
>  [1] grid      tools     tcltk     stats     graphics  grDevices utils
> datasets  methods   base
>
> other attached packages:
>  [1] hugene10sttranscriptcluster.db_5.0.1 org.Hs.eg.db_2.4.1
>   RColorBrewer_1.0-2
>  [4] gplots_2.7.4                         caTools_1.10
>   bitops_1.0-4.1
>  [7] gdata_2.8.0                          gtools_2.6.2
>   oneChannelGUI_1.14.2
> [10] RaExExonProbesetLocation_1.0.0       MoExExonProbesetLocation_1.0.0
>   HuExExonProbesetLocationHg19_0.0.2
> [13] edgeR_1.6.2                          IRanges_1.6.0
>    preprocessCore_1.10.0
> [16] GOstats_2.14.0                       graph_1.26.0
>   Category_2.14.0
> [19] AnnotationDbi_1.10.0                 tkWidgets_1.26.0
>   DynDoc_1.26.0
> [22] widgetTools_1.26.0                   affylmGUI_1.22.0
>   affyio_1.16.0
> [25] affy_1.26.0                          limma_3.4.0
>    pd.hugene.1.0.st.v1_0.0.1
> [28] pdInfoBuilder_1.12.0                 oligo_1.12.0
>   oligoClasses_1.10.0
> [31] affxparser_1.20.0                    RSQLite_0.8-4
>    DBI_0.2-5
> [34] Biobase_2.8.0
>
> loaded via a namespace:
>  [1] annotate_1.26.0   Biostrings_2.16.0 genefilter_1.30.0 GO.db_2.4.1
> GSEABase_1.10.0   RBGL_1.24.0       splines_2.11.0
>  [8] survival_2.35-8   XML_3.1-0         xtable_1.5-6
>
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