[BioC] reading data from Beadarray into R
Hajar Hassani Lahsinoui
hajar.hassani at gmail.com
Thu Sep 30 21:33:34 CEST 2010
Hi Steve, Martin and Matt,
Thanks again for all the help.
I found the perBeadFiles in the data set!
Hajar
On Sep 30, 2010, at 3:30 AM, Matthew Ritchie wrote:
> 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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