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

[André Chanderbali]

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 at botany.ufl.edu
>> _______________________________________________
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>
> Naomi S. Altman                                814-865-3791 (voice)
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> Bioinformatics Consulting Center
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