[BioC] reading Aglilent 60mer oligo data files into limma

Gordon K Smyth smyth at wehi.EDU.AU
Mon Nov 1 12:23:20 CET 2004

> Date: Fri, 29 Oct 2004 11:43:22 -0400
> From: Andr? Chanderbali <achander at botany.ufl.edu>
> Subject: [BioC] reading Aglilent 60mer oligo data files into limma
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <43B19B22-29C1-11D9-806C-0003938C4B2C at 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


> 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 at botany.ufl.edu

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