[BioC] ReadAffy Error: new versions causing problems?

[Ben Bolstad]

These errors are typically caused by a mismatch between your version of
affy and your version of affyio. Given that you note that it works fine
using affy 1.12.0, this likely means you are uing an older affyio (not
the one from the current BioC 2.0 release)

Ben



On Mon, 2007-05-28 at 16:43 +0000, Julien Gagneur wrote:
> 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.
> 
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