[BioC] sampleSheet problem in beadArray

Christine Stansberg [guest] guest at bioconductor.org
Thu Aug 14 15:16:40 CEST 2014

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.


 -- output of sessionInfo(): 

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> 

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