[BioC] reading data from Beadarray into R

Jenny Drnevich drnevich at illinois.edu
Wed Sep 29 23:47:59 CEST 2010


Hi Hajar,

There's your problem. You don't have a file just called 
"beadTypeFile.txt". To read in any one of these files, you have to 
specify it EXACTLY by name:

 > targets <- read.table("5513091009_A_beadTypeFile.txt")

HTH,
Jenny

At 04:38 PM 9/29/2010, Hajar Hassani Lahsinoui wrote:
>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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> >



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