ReadGPR.R

library(limma) sessionInfo()

1. 0 Set up directories

auxillaryDir <- "/Volumes/HD2/Data/Nutrigenomics/MultipleScans/Auxillary" dataDir <- "/Volumes/HD2/Data/Nutrigenomics/MultipleScans/GPR" plotDir <- "DiagnosticImages"

1. 1) load targets and data

targets <- readTargets(dir(auxillaryDir), path=auxillaryDir)

type <- "median" source.type <- switch(type,

      mean   = "genepix",
      median = "genepix.median"
      )

print(paste("source =",source.type))

RG <- read.maimages(targets$Filename, path = dataDir, source=source.type, names=paste(targets$Filetype, targets$Scan),

                   wt.fun=wtflags(0))

RG$printer <- getLayout(RG$genes)