[BioC] Error: read.affybatch

[S Peri]

hi Ben, 
 
All my CEL files are with .CEL extension. They are not
text files. When I open them they are exactly in the
same format as CEL (starting with [CEL] header).

In addition to all the CEL files in the directory I
have all my CEL files, I had two other files with
names Cel_key.xls and breastCancerData_2.xls which I
changed them to Cel_key.txt and
breastCancerData_2.txt(both as tab delimited txt
files).

Pls. suggest what I am doing wrong.

Thanks
SP

--- Ben Bolstad <bolstad at stat.berkeley.edu> wrote:
> how come your cel files end in .txt?  are you sure
> they are cel files
> and not something else? What do you see if you open
> up one of the files.
> 
> Also, for most people ReadAffy() is a better way
> then calling
> read.affybatch() since it will create the phenodata
> automatically.
> 
> Ben
> 
> 
> 
> 
> 
> On Wed, 2004-06-30 at 20:38, S Peri wrote:
> > Hello group, 
> >  I am trying to read my cel files using
> read.affybatch
> > method.
> > 
> > I stored all my cel files, probe information file
> and
> > experiment file in one directory. 
> > 
> > I used the following commands:
> > 
> > >fls = list.files()
> > >ab = read.affybatch(filenames=fls)
> > Error in initialize(value, ...) : Is
> > breastCancerData_2.txt really a CEL file? tried
> > reading as text, gzipped text and binary
> > In addition: Warning message: 
> > Incompatible phenoData object. Created a new one.
> >  in: read.affybatch(filenames = fls) 
> > 
> > 
> > I am getting the above error.  What could be
> > happening. 
> > I am trying to analyze Mike West and Nievens
> Breast
> > cancer affy data (Duke University). 
> > 
> > Could any one please help me what is wrong here
> and
> > also how does a phenoData file look like. What is
> > phenoData. 
> > 
> > Please help. 
> > 
> > thank you
> > 
> > SP
> > 
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
> >
>
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> -- 
> Ben Bolstad <bolstad at stat.berkeley.edu>
> http://www.stat.berkeley.edu/~bolstad
> 
>