[BioC] Error: read.affybatch

[S Peri]

After reading a ?read.phenoData I tried the following:

> read.phenoData(filename = "Cel_key.txt")
Error in scan(file = file, what = what, sep = sep,
quote = quote, dec = dec,  : 
        line 3 did not have 7 elements


cel_key.txt file looks like this:


CEL file name	ER status	LN status
Nevins4	pos	pos
Nevins5	pos	pos
Nevins6	pos	pos
Nevins7	neg	pos
Nevins8	neg	pos
Nevins9	neg	pos
Nevins11	neg	pos
Nevins13	pos	pos
Nevins19	pos	pos
Nevins20	pos	pos
Nevins21	pos	neg
Nevins22	pos	neg
Nevins23	neg	neg
Nevins24	neg	neg
Nevins25	neg	neg
Nevins26	neg	neg
Nevins36	pos	neg
Nevins37	pos	neg
Nevins38	pos	neg
Nevins39	pos	neg
Nevins40	pos	pos
Nevins41	pos	pos
Nevins42	neg	neg
Nevins43	neg	neg
Nevins46	pos	pos
Nevins47	neg	pos
Nevins48	neg	neg
Nevins97	neg	neg
Nevins98	neg	pos



thanks
SP

--- S Peri <biocperi at yahoo.com> 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
>