[BioC] reading data from Beadarray into R

[Hajar Hassani Lahsinoui]

Hi Jenny and Steve,

Thank you for your help clearing things up!

At least it recognizes the file now. Do you know what R means by line 2?:

targets <- read.table("5513091009_A_beadTypeFile.txt")
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  : 
  line 2 did not have 3 elements

Hajar

On Sep 29, 2010, at 11:47 PM, Jenny Drnevich wrote:

> 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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>> >
>