[BioC] sampleSheet problem in beadArray

[James W. MacDonald]

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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