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

[Tobias Petri]

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