[BioC] reading data from Beadarray into R

[Hajar Hassani Lahsinoui]

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: 


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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