Dear All,

I'm hoping to use beadarray to process illuminaHT-12 v4 expression data (just one chip) that was generated using iScan. I have .locs files and .tif files for both swath1 and swath2 and have used processSwathData() to split the .txt file appropriately. I'm now struggling to execute the readIllumina() function for some reason (below). Do i need to modify my sampleSheet following processSwathData() to take into account the fact that I now have two .txt files for each array? I can't get passed the error message below.



> processSwathData(inputDir = "data/9259561003", outputDir = "data/9259561003", twoColour=NULL, textstring="_perBeadFile.txt", segmentHeight=326, segmentWidth=397, fullOutput=TRUE, newTextString=".txt")

9259561003_A
9259561003_B
9259561003_C
9259561003_D
9259561003_E
9259561003_F
9259561003_G
9259561003_H
9259561003_I
9259561003_J
9259561003_K
9259561003_L



> sampleSheetFile <- paste("data/9259561003", "/sampleSheet.csv", sep = "")
> readLines(sampleSheetFile)



 [1] "[Header],,,"                                           "Investigator Name,Darren,,"                       "Project Name,RMS Whole Genome Expression Profiling,,"
 [4] "Experiment Name,Chip 1,,"                              "Date,31/05/2013,,"                                     "[Data],,,"
 [7] "Sample_Name,Sample_Group,Sentrix_ID,Sentrix_Position"  "RMS06012,poor,9259561003,A"                           "RMS12038,good,9259561003,B"
[10] "RMS12001,good,9259561003,C"                           "RMS21004,poor,9259561003,D"                           "RMS12039,poor,9259561003,E"
[13] "RMS12016,good,9259561003,F"                           "RMS12032,good,9259561003,G"                           "RMS12041,poor,9259561003,H"
[16] "RMS15003,poor,9259561003,I"                           "RMS20020,good,9259561003,J"                           "RMS20022,good,9259561003,K"
[19] "RMS10025,poor,9259561003,L"



> data <- readIllumina("data/9259561003", sampleSheet = sampleSheetFile, useImages = TRUE, illuminaAnnotation = "Humanv4")

Sample Sheet D:\work\RMS\data\9259561003\sampleSheet.csv will be used to read the data
Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]),  :
  Directory does not exist.

Thanks in advance!

Best wishes,

Darren

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