## ----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]);