[BioC] sampleSheet problem in beadArray

[Mark Dunning]

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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> >
>
>
>
> --
> 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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>
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