# Set the wd:
setwd("C:/BASE/Illumina imports/BeadStudio output")

# Choose the file:
filename <- "gene_profile.csv"

#Set the number of arrays per chip:
arraysPerChip = 8; # 6
columnsPerArray = 8;

# assign the column headers:
headerColumnNames <-c("MIN_Signal","AVG_Signal","MAX_Signal","NARRAYS","ARRAY_STDEV","BEAD_STDEV","Avg_NBEADS","Detection"

illumina <- read.csv(file=paste(getwd(),"/",filename,sep=""),skip=7,header=TRUE,row.name=1)

ncol(illumina)
nrow(illumina)

numData = ncol(illumina) - 
numArrays = numData / columnsPerArray	# 8 data columns per array
numChips = numArrays/arraysPerChip	#

numChips

if numChips%%1 ~= 0
	"ERROR: an incomplete chip is in this file!"

colnames(illumina) -> myCols

#	Derive the Chip names from the colnames:
#	Format of first entry: "MIN_Signal.XXXXXXXXXX_A" ( 10 Xs: maybe different?)

lenFirstData <-nchar(headerColumnNames[1])

chipNums = NULL
arrayNames = NULL

# Derive names of arrays:
for (k in 1:numChips){
		
	# Get the numbers of the chips:
colNum = 1 + (k-1)* (arraysPerChip *columnsPerArray)
chipNums = c(chipNums, substr(myCols [colNum],lenFirstData+2,nchar(myCols[colNum])-2))

	# Get names of all the arrays
	labels = c("A","B","C","D","E","F","G","H")
	labels = labels[1: arraysPerChip]
	arrayNames = c(arrayNames, paste(chipNums[k],labels,sep="_"))
}
chipNums
arrayNames


# output arrays (groups of columnsPerArray columns, plus gene names)
for (k in 1:length(arrayNames))
{
	outputCols <- c(1: columnsPerArray) + columnsPerArray * (k-1)
	outputData <- illumina[,outputCols]
	outputData <- cbind(rownames(illumina),outputData) 

	colnames(outputData) <- as.character(c("TargetID",headerColumnNames))

	write.table(outputData,file = paste(arrayNames[k],".txt",sep=""),sep = "\t",row.names=FALSE,na="")
}