[BioC] gcrma/rma using drosophila CEL files, VECTOR_ELT() problem

[Tobias Petri]

UPDATE / SOLVED:

A variant of the problem has been described previously. I solved it by
installing the current R-2.9.1 and bioconductor packages. The config ist
now:

> sessionInfo()
R version 2.9.1 (2009-06-26)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] drosophila2probe_2.4.0 AnnotationDbi_1.6.1    drosophila2cdf_2.4.0 
[4] gcrma_2.16.0           Biostrings_2.12.8      IRanges_1.2.3        
[7] affy_1.22.0            Biobase_2.4.1          limma_2.18.2         

loaded via a namespace (and not attached):
[1] DBI_0.2-4            RSQLite_0.7-1        affyio_1.12.0      
[4] preprocessCore_1.6.0 splines_2.9.1        tcltk_2.9.1        
[7] tools_2.9.1

Tobias Petri schrieb:
> Hi,
>
> I have several affy drosophila v2 genome chip CEL files which I want to
> read-in using 'affy'. I get the following error with
> pure rma() and gcrma(). Also the use of expresso for conversion to an
> ExpressionSet fails. The basic call is:
>
> library(affy)
> library(gcrma)
>
>   
>> r <- ReadAffy(celfile.path="fly_affy/CEL/")
>>     
>
>   
>> r
>>     
> AffyBatch object
> size of arrays=732x732 features (17 kb)
> cdf=Drosophila_2 (18952 affyids)
> number of samples=20
> number of genes=18952
> annotation=drosophila2
> notes=
>
>   
>> eset_gcrma <- gcrma(r)
>>     
> Adjusting for optical effect....................Done.
> Computing affinities[1]
> Adjusting for non-specific binding....................Done.
> Normalizing
> Calculating Expression
> Fehler in rma(object, subset = subset, background = FALSE, normalize =
> normalize,  :
>   VECTOR_ELT() can only be applied to a 'list', not a 'character'
>
> Does somebody know why the conversion fails?
>
> Regards,
> Tobias
>
>   
>> sessionInfo()
>>     
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base    
>
> other attached packages:
> [1] drosophila2probe_2.3.0 gcrma_2.14.1           matchprobes_1.14.1   
> [4] drosophila2cdf_2.3.0   affy_1.20.2            Biobase_2.2.2        
> [7] limma_2.16.5         
>
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1        preprocessCore_1.4.0
>
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>
>   


-- 


   ===============================================================
   Tobias Petri                               
   ===============================================================
   LFE Bioinformatik
   Amalienstr. 17
   80333 München, DE
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   mail  :  tobias.petri at bio.ifi.lmu.de        
   phone :  +49 89 2180 4042                    
   web   :  http://www.bio.ifi.lmu.de/mitarbeiter/tobias-petri   
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