You are trying to read in CSV files.  Beadarray isn't really meant to handle
these (as far as I know) because they have already been summarized by
Illumina's software.  The text files that 'beadarray' expects have one line
per bead, usually with X and Y coordinates as well.

I can send you code to handle this type of input, but really you are better
off using the raw data (if these are expression arrays) or the .idat files
(if these are SNP or methylation arrays) and my intention is to make the
latter more amenable to both by using oligoClasses in the near future.
 Illumina's file format nightmare is not doing anyone any favors, IMHO.

--tim



On Mon, Dec 6, 2010 at 3:18 AM, Daniela Albrecht <
daniela.albrecht@biocontrol-jena.com> wrote:

> Dear bioconductor people.
>
> I am using the beadarray package for working with Illumina bead data. In
> beadarray version 1.4 following code works fine for reading the data:
>
> /targets=read.table(file="./5645810041_txt-Datein/targets.txt",header=T)
>
> a<-readIllumina(path="./5645810041_txt-Datein",arrayNames=targets[,"ArrayName"],useImages=F,metrics=T,
>             textType=".csv",metricsFile="./5645810041/Metrics.txt")/
>
> With the new beadarray version 2.02. It does not work anymore. With a
> simplified code line
>
> /a<-readIllumina(useImages=F,metrics=T)/
>
> it says cannot open path/5645810041_txt-Datein/NA no such file or
> directory.
>
> How do I have to specify the filename, so it does not want to open a
> file named "NA.txt"? By the way, if I rename my first datafile in
> NA.txt, it says
>
> Unknown input format!
> Expected 4 columns for single channel data or 7 columns for two channel
> data
>
> This is how my file looks like (I also tried to change the , into tab
> but it does not work either:
>
> Illumicode,N,Mean GRN,Dev GRN
> 10008,36,646,124
> 10010,17,91,21
> 10014,12,72,11
> 10017,19,83,17
> 10019,30,216,39
> ...
>
> Thanks in advance for your help Daniela
>
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>
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-- 
If people do not believe that mathematics is simple, it is only because they
do not realize how complicated life is.
John von Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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