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

[Steve Lianoglou]

Hi Jessica,

On Aug 27, 2009, at 12:49 PM, 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.

First thing that comes to mind (since it works on windows and not  
linux) is that you should just double check that the letter casing in  
your file and dir names.

The windows filesystem is not case sensitive (last I knew) and linux is.

So:

> I start by creating the dirPath:
>
> dir <- “~/Desktop/Maq50bp/Map_files”

Imagine your directory was actually called "~/Desktop/Maq50bp/map_files”

Your command would work in windows, but not in linux.

Just something you might want to check real quick before starting to  
pull any hair out.

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact