reading Aglilent 60mer oligo data files into limma
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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia
> 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
Genetics limma oligo Genetics limma oligo • 748 views
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@andre-chanderbali-991
Last seen 9.6 years ago
Thanks Naomi, I think I figured it out...the filenames in the targets file must have ".txt" extensions but the actual files should not. Otherwise R looks for "filename.txt.txt" Andre On Monday, November 1, 2004, at 12:23 PM, Naomi Altman wrote: > Hi Andre, > > We did not have any problems doing this here. Of course, I think Tony > actually typed in the file names. > > --Naomi > > At 11:43 AM 10/29/2004 -0400, you wrote: >> 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? >> >> 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 >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Bioinformatics Consulting Center > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111
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