[BioC] R-2.9.1/Bioconductor on RedHat Enterprise 5.3

[Martin Morgan]

Hi Jessica --

Jessica Hunter wrote:
> Hello all. I am a long-term R user who has recently switched platforms from Windows to Linux and I am having a hard time with the syntax difference.  I am stuck on something that is likely simple, but I am stuck all the same.  I have aligned short reads using Maq 0.7.1 in RedHat and I have the ‘map’ output files as well as the ‘map.txt’ files obtained by mapview.  I am trying to input the files into Bioconductor using ShortReads, but I can’t seem to read the files in.  I can get ‘readAligned’ to work on Windows, but I need the memory from my Linux computer.   
> 
>  
> 
> I start by creating the dirPath:
> 
> dir <- “~/Desktop/Maq50bp/Map_files”
> 
> aln <- readAligned(dir,”s_1_sequence.map”,”MAQMap”)

what does list.files(dir, "s_1_sequence.map") say? Perhaps you want 
"^s_1_sequence.map$"

I think the error below is really saying that dir/pattern matches more 
than one file.

Also, you might try starting R with the 'locale' set to 'C'; those 
non-ascii characters in your message make me nervous. Something along 
the lines of, from a bash command line

% LC_ALL=C R

Martin

> 
>  
> 
> Using this, I get an error that ‘pattern’ must be ‘character(1)’.  Alternately, I define pattern by:
> 
>  
> 
> pattern <- “s_1_sequence.map”
> 
> aln <- readAligned(dir,pattern,”MAQMap”)
> 
>  
> 
> And I get the error that my directory is not a readable directory.  Though I have the right permissions for this directory.
> 
>  
> 
> Any insight would be greatly appreciated.
> 
>  
> 
> Jessica
> 
>  
> 
> Jessica Ezzell Hunter, MS PhD
> 
> Postdoctoral Fellow
> Department of Behavioral Neuroscience
> 
> Oregon Health & Science University
> 3181 SW Sam Jackson Park Road
> 
> L470
> Portland, OR 97239
> 
> (503) 220-8262 x51988
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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