[BioC] reading data from Beadarray into R

[Hajar Hassani Lahsinoui]

Hi,

I think so, I removed a few files, so there are 6 now.
This is what I get:

dir()
[1] "5513091009_A_beadTypeFile.txt" "5513091009_B_beadTypeFile.txt" "5513091009_C_beadTypeFile.txt" "5513091009_D_beadTypeFile.txt" "5513091009_E_beadTypeFile.txt" "5513091009_F_beadTypeFile.txt"
> 5513091009_A_beadTypeFile.txt
5513091009_B_beadTypeFile.txt
5513091009_C_beadTypeFile.txt
5513091009_D_beadTypeFile.txt
5513091009_E_beadTypeFile.txt
5513091009_F_beadTypeFile.txt

Hajar

On Sep 29, 2010, at 11:30 PM, Jenny Drnevich wrote:

> 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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>