[BioC] rma error on an affyBatch from ArrayExpress?

[Martin Morgan]

Hi Ross -- affy and affyio are out of date relative to preprocessCore.

  source('http://bioconductor.org/biocLite.R')
  old.packages(repos=biocinstallRepos())
  update.packages(repos=biocinstallRepos())

Martin

Ross Lazarus wrote:
> While testing ArrayExpress with E-GEOD-17215 I see
> 
> Error in rma(ae) :
> VECTOR_ELT() can only be applied to a 'list', not a 'character'
> 
> being thrown by rma applied to the downloaded AffyBatch - shown below. Not
> sure whether this is a problem with the source data at ArrayExpress or
> stupidity on my own part, but I can't find any sign of this specific error
> text in any relevant google results - suggestions appreciated. R2.9.2 -
> sessionInfo() at end of post:
> 
> ========================
> R version 2.9.2 (2009-08-24)
> Copyright (C) 2009 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>   Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
> 
>> library(ArrayExpress)
> Loading required package: Biobase
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
> Loading required package: affy
> Loading required package: limma
> Loading required package: XML
>> ae = ArrayExpress('E-GEOD-17215',save=T)
> trying URL '
> ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-17215/E-GEOD-17215.raw.zip
> '
> (----normal AE download stuff deleted-----)
> Read 48 items
> Read 48 items
>> ls()
> [1] "ae"         "mapCdfName"
>> ae
> AffyBatch object
> size of arrays=744x744 features (10794 kb)
> cdf=HT_HG-U133A (22277 affyids)
> number of samples=6
> number of genes=22277
> annotation=hthgu133a
> notes= E-GEOD-17215
>         E-GEOD-17215
>         NA
>         unknown_experiment_design_type
>         NULL
>> rma(ae)
> Background correcting
> Normalizing
> Calculating Expression
> Error in rma(ae) :
>   VECTOR_ELT() can only be applied to a 'list', not a 'character'
> 
>> sessionInfo()
> R version 2.9.2 (2009-08-24)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] hthgu133acdf_2.4.0 ArrayExpress_1.2.2 XML_1.99-0
> limma_2.18.3
> [5] affy_1.20.0        Biobase_2.4.1
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1        preprocessCore_1.6.0 tools_2.9.2
> 
> 
> ==============
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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