[BioC] reading data from Beadarray into R

Martin Morgan mtmorgan at fhcrc.org
Thu Sep 30 00:37:28 CEST 2010


On 09/29/2010 03:15 PM, Hajar Hassani Lahsinoui wrote:
> 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

Hi Hajar --

I think that what you are trying to do is to read a 'targets' file,
with columns that describe (a) the file name; and (b) the sample
associated with the file. But what you are actually doing is trying to
read one of the data files itself.

Time to back up and read the beadarray vignettes a second time.

  http://bioconductor.org/packages/2.6/bioc/html/beadarray.html

Martin

> 
> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
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>>>>
>>
> 
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