[BioC] package affy / biobase problem with function "geneNames"

[Martin Morgan]

On 04/04/2014 08:08 AM, BEN HAMDA Cherif wrote:
> Hello,
>
> after updating all packages. I have a problem when i want normalize my data
> !

This is a package version mismatch. Biobase is from Bioconductor version 2.11, 
affy and BiocInstaller from version 2.10. I think

   library(BiocInstaller)
   biocLite("BiocUpgrade")

will update all packages to version 2.11.

Really you should update to the current R (3.0.3) and Bioconductor (2.13) or 
wait until after April 15 and update to R 3.1.0 and Bioconductor 2.14.

Martin

>
> and the error message is  :
>
>> eset <- rma(rawdata)
> Error in rma(rawdata) : could not find function "geneNames"
>
> Someone can help me Please , Thank you very much
>
> Best
> Cherif
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8    LC_NUMERIC=C            LC_TIME=C
>   [4] LC_COLLATE=en_US.UTF-8  LC_MONETARY=C           LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C              LC_NAME=C               LC_ADDRESS=C
> [10] LC_TELEPHONE=C          LC_MEASUREMENT=C        LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] hgu133plus2cdf_2.11.0 AnnotationDbi_1.18.4  simpleaffy_2.34.0
> [4] gcrma_2.30.0          genefilter_1.38.0     affy_1.34.0
> [7] Biobase_2.18.0        BiocGenerics_0.4.0    limma_3.12.3
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.24.0         annotate_1.34.1       BiocInstaller_1.4.9
>   [4] Biostrings_2.24.1     DBI_0.2-7             IRanges_1.14.4
>   [7] preprocessCore_1.18.0 RSQLite_0.11.4        splines_2.15.1
> [10] stats4_2.15.1         survival_2.37-7       tools_2.15.1
> [13] XML_3.98-1.1          xtable_1.7-1          zlibbioc_1.2.0
>
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>
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