[BioC] Limma: Trying to read in imagene files

Gordon Smyth smyth at wehi.EDU.AU
Sat Jan 5 08:04:12 CET 2008

Dear Sally,

The limma output shows that it has read all your ImaGene files 
correctly. I suspect that your targets file has a spurious blank line 
at the end of the file that you need to remove. This causes limma to 
try to read a non-existent file with name "".

Best wishes

>Date: Thu, 03 Jan 2008 11:33:24 -0800
>From: Sally <sagoldes at shaw.ca>
>Subject: [BioC] Limma: Trying to read in imagene files
>To: bioconductor at stat.math.ethz.ch
>Message-ID: <000801c84e3f$a7ce9920$263f4518 at sghome>
>Content-Type: text/plain
>I've been trying to troubleshoot this for a couple of days and can't 
>find the problem.  I wasn't having this problem before so I don't 
>know what has changed. I am getting the following error message:
> > RG<-read.imagene(files,wt.fun=myfun)
>Read header information
>Read 215s48Cy3flagvalueschanged.txt
>Read 215s48Cy5flagvalueschanged.txt
>Read 225s48Cy3flagvalueschanged.txt
>Read 225s48Cy5flagvalueschanged.txt
>Read 234s48Cy3flagvalueschanged.txt
>Read 234s48Cy5flagvalueschanged.txt
>Read 196s48Cy3flagvalueschanged.txt
>Read 196s48Cy5flagvalueschanged.txt
>Read 199s48Cy3flagvalueschanged.txt
>Read 199s48Cy5flagvalueschanged.txt
>Read 217s48Cy3flagvalueschanged.txt
>Read 217s48Cy5flagvalueschanged.txt
>Error in if (skip > 0) readLines(file, skip) : argument is of length zero
>In addition: Warning messages:
>1: In file(file, "r") :
>   file("") only supports open = "w+" and open = "w+b": using the former
>2: In readImaGeneHeader(fullname) :
>   End of file encountered before End Header
>3: In file(file, "r") :
>   file("") only supports open = "w+" and open = "w+b": using the former
> >
>My targets file looks like this
>       SlideNumber Name FileNameCy3 FileNameCy5 Cy3 Cy5
>       215 215s48 215s48Cy3flagvalueschanged.txt 
> 215s48Cy5flagvalueschanged.txt infected control
>       225 225s48 225s48Cy3flagvalueschanged.txt 
> 225s48Cy5flagvalueschanged.txt control infected
>       234 234s48 234s48Cy3flagvalueschanged.txt 
> 234s48Cy5flagvalueschanged.txt infected control
>       196 196s48 196s48Cy3flagvalueschanged.txt 
> 196s48Cy5flagvalueschanged.txt control infected
>       199 199s48 199s48Cy3flagvalueschanged.txt 
> 199s48Cy5flagvalueschanged.txt infected control
>       217 217s48 217s48Cy3flagvalueschanged.txt 
> 217s48Cy5flagvalueschanged.txt control infected

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