Entering edit mode
> Date: Fri, 29 Oct 2004 11:43:22 -0400
> From: Andr? Chanderbali <achander@botany.ufl.edu>
> Subject: [BioC] reading Aglilent 60mer oligo data files into limma
> To: bioconductor@stat.math.ethz.ch
> Message-ID: <43B19B22-29C1-11D9-806C-0003938C4B2C@botany.ufl.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Dear All,
>
> I'm have data txt files from Agilent's 60mer Arabidopsis slides that
> were created using Agilent's feature extraction software, and am
trying
> to read them into limma (using Bioconductor) and have encountered
the
> following problem.
>
> I can read in my targets file just fine but with the follow up
command:
>
> "RG <- read.maimages(files=targets$FileName, source="agilent"')"
>
> I get the following:
>
> "Error in grep(pattern, x, ignore.case, extended, value, fixed) :
> invalid command"
>
> Does anyone know why this is and how it can be overcome?
No this is not a known problem (other it would get fixed). You need
to give more information that
this. Version of limma? Did you get any output other than that
given? Can you give the leading
lines of your first data file? [e.g., by
writeLines(readLines(targets$FileName[1],n=20)) at the R
prompt]
Gordon
> Thank you,
>
> Andre Chanderbali
> Post Doctoral Associate
> Florida Museum of Natural History
> and the Genetics Institute
> Dickinson Hall
> PO Box 117800
> University of Florida
> Gainesville, FL 32611-7800
>
> phone: 352-392-1721 ext. 500
> fax: 352-846-2154
> email: achander@botany.ufl.edu