[BioC] reading data from Beadarray into R

Thu Sep 30 03:30:22 CEST 2010

Hi Hajar,

Just to follow up on Martin's message, it is not clear that you are
dealing with raw bead-level data, so beadarray might not be of much use to
you.

Illumina's iScan outputs files with the extension '_perBeadFile.txt' for
this kind of data.  I believe files with the extension '_beadTypeFile.txt'
contain summary data.  The beadarray package supports either raw
bead-level data in text format or summary data output by
BeadStudio/GenomeStudio.

Best wishes,

Matt

> 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
>>>>>>
>>>>>>
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>>>>>
>>>
>>
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>
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