[BioC] RMA normalization issue

[Hervé Pagès]

Hi Fuying,

Your version of affy is not matching your version of R/Bioconductor.
Please install/reinstall/update your packages following our instructions
here:

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

Failing to do so will give you no end of troubles...

Cheers,
H.


Fuying Gao wrote:
> Dear List,
> 
> I got error as follows when normolizing a AffyBatch Object (400 samples) 
> with R 2.9.0.  It works on an old version of R, R 2.6.1, on another 
> computer but the computer can not handle so many samples due to memory 
> issue.
> There is no problem to read in the cel files from both versions of R.
> 
> 
> Error in rma(dat) :
>   VECTOR_ELT() can only be applied to a 'list', not a 'character'
> 
> #dat is the AffyBatch Object
> 
> #session info is as follows (got the above error):
> 
>> sessionInfo()
> 
> R version 2.9.0 (2009-04-17)
> x86_64-redhat-linux-gnu
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
>  [1] hgu133acdf_2.2.0     annaffy_1.12.1       KEGG.db_2.2.0
>  [4] GO.db_2.2.0          RSQLite_0.6-8        DBI_0.2-4
>  [7] AnnotationDbi_1.4.3  gplots_2.6.0         gdata_2.4.2
> [10] gtools_2.5.0         MASS_7.2-46          RColorBrewer_1.0-2
> [13] affyPLM_1.16.0       simpleaffy_2.16.0    gcrma_2.12.1
> [16] matchprobes_1.12.0   genefilter_1.20.0    survival_2.35-4
> [19] affy_1.18.1          preprocessCore_1.2.0 affyio_1.8.0
> [22] marray_1.18.0        limma_2.14.4         Biobase_2.2.2
> 
> loaded via a namespace (and not attached):
> [1] annotate_1.18.0
> 
> 
> 
> 
> 
> #session info is as follows (no error, an older version R):
> 
>> sessionInfo()
> 
> R version 2.6.1 (2007-11-26)
> i386-pc-mingw32
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     
> datasets  methods   base
> 
> other attached packages:
>  [1] hgu133plus2cdf_2.0.0 annaffy_1.10.0       KEGG_2.0.0           
> GO_2.0.0
>  [5] gplots_2.3.2         gdata_2.3.1          gtools_2.4.0         
> MASS_7.2-38
>  [9] RColorBrewer_1.0-1   affyPLM_1.14.0       simpleaffy_2.14.02   
> gcrma_2.10.0
> [13] matchprobes_1.10.0   genefilter_1.16.0    survival_2.34        
> affy_1.16.0
> [17] preprocessCore_1.0.0 affyio_1.6.0         marray_1.16.0        
> limma_2.12.0
> [21] Biobase_1.16.0
> 
> 
> It would be great if someone could help figure out what caused the error.
> Thank you!
> 
> Fuying Gao
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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