[BioC] reading data from Beadarray into R

Jenny Drnevich drnevich at illinois.edu
Wed Sep 29 23:30:21 CEST 2010


Hi,

Just a sanity check - is one of the 14 files you put in the 
experiment folder called "beadTypeFile.txt"?  You can check by doing:

 > setwd( "/Users/hajarhassani/Desktop/Experiment")
 > dir()

This will list out all the file names in the working directory. I 
often do this then copy and paste to make sure I've got a file name correct.

Jenny

At 04:12 PM 9/29/2010, Hajar Hassani Lahsinoui wrote:
>Still not working....
>
>getwd()
>[1] "/Users/hajarhassani/Desktop/Experiment"
>
> > targets <- 
> read.table('/Users/hajarhassani/Desktop/experiment/beadTypeFile.txt')
>Error in file(file, "rt") : cannot open the connection
>In addition: Warning message:
>In file(file, "rt") :
>   cannot open file 
> '/Users/hajarhassani/Desktop/experiment/beadTypeFile.txt': No such 
> file or directory
>
>I put 14 files in the experiment folder. The files look right:
>
>
> >
>
>
>
>Could there be something wrong with the way the files were saved?
>R seems to work just fine with SAMExample practice dataset from bioconductor.
>
>
>
>
>On Sep 29, 2010, at 10:32 PM, Steve Lianoglou wrote:
>
> > Hi,
> >
> > On Wed, Sep 29, 2010 at 4:05 PM, Hajar Hassani Lahsinoui
> > <hajar.hassani at gmail.com> wrote:
> >>
> >> On Sep 29, 2010, at 9:48 PM, Steve Lianoglou wrote:
> >>
> >>> argets = read.table("/Users/hajarhassani/Documents/Image
> >>> Data/5513091009/BeadTypeFile.txt")
> >> Hi Steve,
> >>
> >> You were right:
> >>
> >> file.exists('BeadTypeFile.txt')
> >> [1] FALSE
> >>
> >>> targets = read.table("/Users/hajarhassani/Documents/Image
> >> + Data/5513091009/BeadTypeFile.txt")
> >> Error in file(file, "rt") : cannot open the connection
> >> In addition: Warning message:
> >> In file(file, "rt") :
> >>  cannot open file '/Users/hajarhassani/Documents/Image
> >> Data/5513091009/BeadTypeFile.txt': No such file or directory
> >>
> >> I tried changing the directory to the DVD they gave me the data 
> on (instead of my HD), but still the same message. The thing is 
> that I can open the txt files if I click on them from my HD 
> (Illumicode,N,Mean GRN,Dev GRN), so they must be retreivable...
> >
> > Maybe it's the space-in-the-directory thing.
> >
> > Try creating some "experiment" folder on your desktop and copy all the
> > files you need into it, then:
> >
> > R> targets <- 
> read.table('/Users/hajarhassani/Desktop/experiment/BeadTypeFile.txt')
> >
> > --
> > 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
>
>
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