[BioC] Error: read.affybatch

[Ben Bolstad]

Try either

myData <- ReadAffy()

or

myData <- read.affybatch(files=list.celfiles())


Thanks,

Ben





On Wed, 2004-06-30 at 21:16, S Peri wrote:
> 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
> > > 
> > > _______________________________________________
> > > Bioconductor mailing list
> > > 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
> > 
> >
> 
> _______________________________________________
> Bioconductor mailing list
> 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