[BioC] ReadAffy Error: new versions causing problems?

[Julien Gagneur]

James W. MacDonald <jmacdon at ...> writes:
 
> Hi Boel,
> 
> Boel Brynedal wrote:
> > Dear List,
> > 
> >>raw<-ReadAffy()
> > 
> > Error in read.affybatch(filenames = l$filenames, phenoData = l
> > $phenoData,  :
> >         VECTOR_ELT() can only be applied to a 'list', not a 'char'
> > 
[...]
>
> Also, does
> 
> raw <- ReadAffy(filenames=list.celfiles())
> 
> help?


Dear List,

I have a problem similar to the one raised by Boel but for which list.celfiles()
would not help.

This is what I get under R version 2.5.0 (2007-04-23), x86_64-redhat-linux-gnu
affy 1.14.0:

> a = ReadAffy(filenames="tmp.CEL.gz", celfile.path="data/celfiles", 
verbose=TRUE, compress=TRUE)
1 reading data/celfiles/tmp.CEL.gz ...instantiating an AffyBatch
(intensity a 6553600x1 matrix)...done.
Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData,  :
        VECTOR_ELT() can only be applied to a 'list', not a 'char'



The problem seems to be environment related, everything goes fine under windows,
using R version 2.5.0 (2007-04-23) i386-pc-mingw32, affy 1.14.0.


It may be due to a change in the code of read.affybatch. If I use the
read.affybatch function of affy 1.12.0, the linux problem does not occur any
more. If this helps, I noticed that in the .Call("read_abatch", ...) 'filenames'
used to be a list of vectors and is now only a vector. 

Thanks for your help,

Julien.