[BioC] sampleSheet problem in beadArray

[Christine Stansberg]

Thank you both for your suggestions.

I finally managed to read everything. I first removed the underscore from the data directory, as suggested by Mark, but this did not change anything. I previously tried to place the sampleSheet file both in the data folder and one level up, with no result. The clue was apparently to move the txt data files one level up and avoid a separate file for the data. Do you think that it did not like to have a folder starting with the same number as the data files? I love that the problem is fixed, but i hate not knowing why…

best,
Christine


14. aug. 2014 kl. 17:16 skrev Mark Dunning <mark.dunning at gmail.com>:

> You should probably try renaming the directory 9031292034_data to 9031292034. I don't think it will like directories with an underscore in the name.
> 
> Best wishes,
> 
> Mark
> 
> 
> On Thu, Aug 14, 2014 at 3:12 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
> Hi Christine,
> 
> The error 'Directory does not exist' has nothing to do with the form of
> your sampleSheet, but instead means that there is either no such file, or
> no such directory. You need to ensure the path you are using is correct.
> 
> Best,
> 
> Jim
> 
> 
> 
> 
> On Thu, Aug 14, 2014 at 9:16 AM, Christine Stansberg [guest] <
> guest at bioconductor.org> wrote:
> 
> > Dear all,
> >
> > this is my first time with bead array and i have been struggling with the
> > sampleSheet for a while now, see error message below (...directory does not
> > exist). I am trying to read bead level intensities from one Human HT12
> > chip, without the images, using readIllumina. If i omit the sampleSheet,
> > BeadArray is able to read my data, so they should be OK. I am also able to
> > read the data from the BeadArrayUseCases - including the sampleSheet. I
> > have taken great care to make sure my sampleSheet-file is identical to the
> > one from the UseCase, but still i get the error message reported below.
> >
> > I am really frustrated and cannot understand why my file does not work
> > when the UseCase one does and would be really grateful for comments.
> >
> > Best,
> > Christine
> >
> >  -- output of sessionInfo():
> >
> > input:
> > NingDataSample
> > =readIllumina(dir="/Users/femcs/Documents/Bioinfo/Bioconductor/NingLu/9031292034_data",
> >                          sectionNames = NULL,
> >                          useImages = FALSE,
> >                          illuminaAnnotation ='Humanv4')
> >
> > output WITH sample sheet:
> > Sample Sheet /Users/femcs/Documents/Bioinfo/Bioconductor/SampleSheet.csv
> > will be used to read the data
> > Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]),
> >  :
> >   Directory does not exist.
> 
> 
> > output WITHOUT sampleSheet structure of object;
> > > str(NingData)
> > Formal class 'beadLevelData' [package "beadarray"] with 4 slots
> >   ..@ beadData      :List of 12
> >   .. ..$ 9031292034_A_perBeadFile:List of 4
> >   .. .. ..$ ProbeID:<environment: 0x7fb615574fc8>
> >   .. .. ..$ GrnX   :<environment: 0x7fb61555b158>
> >   .. .. ..$ GrnY   :<environment: 0x7fb615536a30>
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
> > _______________________________________________
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> > Search the archives:
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> >
> 
> 
> 
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
> 
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