## ----eval=FALSE---------------------------------------------------------------
# tiff <- readTIFF()
# data <- readBeadLevelTextFile()

## ----eval=FALSE---------------------------------------------------------------
# bg <- illuminaBackground(tiff, data[,3:4])
# tiffSharp <- illuminaSharpen(tiff)
# fg <- illuminaForeground(tiffSharp, data[,3:4])
# finalIntensity <- fg - bg

## ----eval=FALSE---------------------------------------------------------------
# BLData <- new(Class = "beadLevelData")
# BLData <- insertBeadData(BLData, array = 1, what = "Grn", data = finalIntensity)

## ----eval=FALSE---------------------------------------------------------------
# BLData <- readIllumina()
# BLData <- insertBeadData(BLData, array = 1, what = "Grn", data = finalIntensity)
# BLData <- insertBeadData(BLData, array = 1, what = "GrnLog", data = log2(finalIntensity))
# 

## ----eval=FALSE---------------------------------------------------------------
# bg <- medianBackground(tiff, data[,3:4]);