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

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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.
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> 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
>


==============

-- 
Ross Lazarus MBBS MPH
Associate Professor, Department of Population Medicine; Director of
Bioinformatics, Channing Laboratory
181 Longwood Ave., Boston MA 02115, USA.
Tel: +617 525 2730  Fax: +617 525 0958

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