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run_affyAnalysisQC.R
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run_affyAnalysisQC.R
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#=============================================================================#
# ArrayAnalysis - affyAnalysisQC #
# a tool for quality control and pre-processing of Affymetrix array data #
# #
# Copyright 2010-2011 BiGCaT Bioinformatics #
# #
# Licensed under the Apache License, Version 2.0 (the "License"); #
# you may not use this file except in compliance with the License. #
# You may obtain a copy of the License at #
# #
# http://www.apache.org/licenses/LICENSE-2.0 #
# #
# Unless required by applicable law or agreed to in writing, software #
# distributed under the License is distributed on an "AS IS" BASIS, #
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. #
# See the License for the specific language governing permissions and #
# limitations under the License. #
#=============================================================================#
version_nb <- "1.0.0"
cat("Script run using R version ",R.Version()$major,".",R.Version()$minor,
" and affyAnalysisQC version_",version_nb,"\n",sep="")
#set memory to maximum on windows 32bit machines
if(length(grep("w32",R.Version()$os,fixed=TRUE))>0) memory.size(4095)
###############################################################################
# Load R libraries and affyAnalysisQC functions #
###############################################################################
require("affy", quietly = TRUE)
require("affycomp", quietly = TRUE)
require("affyPLM", quietly = TRUE)
require("affypdnn", quietly = TRUE)
require("bioDist", quietly = TRUE)
require("simpleaffy", quietly = TRUE)
require("affyQCReport", quietly = TRUE)
require("plier", quietly = TRUE)
if(exists("samplePrep")) require("yaqcaffy", quietly = TRUE)
require("gdata", quietly = TRUE) #trim function
require("gplots", quietly = TRUE) #heatmap.2 functions
print("Libraries have been loaded")
reload <- function() {
source(paste(SCRIPT.DIR,"functions_processingQC.R",sep=""))
source(paste(SCRIPT.DIR,"functions_imagesQC.R",sep=""))
print ("Functions have been loaded")
}
reload();
if(!exists("rawData")) { # this is the case when the script is run locally
setwd(DATA.DIR)
##-- check if is oligo, set global variable isOligo (turn this into function?!?!) (remove global variable!!!!!!!!!)
##copied, inserted, and modified (as indicated) from processFilesQC_web.R - temp fix
#print(DATA.DIR)
filenameindex <- grep("[.CEL]$", dir(), fixed=FALSE, ignore.case=TRUE)[1] #modified line
print(dir()[filenameindex])
if(!is.na(filenameindex)){
#print("going to check oligo")
filename <- dir()[filenameindex];
res <- tryCatch( ReadAffy(filenames=filename) , warning = function(e){e$message}, error = function(e){e$message})
print(res)
if(class(res)=="AffyBatch")
isOligo <- FALSE
else
isOligo <- grepl("oligo", res, ignore.case=TRUE)
#print(isOligo)
} else {
stop("No .cel file found in the specified directory");
}
if(isOligo){
#source("http://bioconductor.org/biocLite.R")
require("oligo") #asklars
print("reading affy with oligo")
#print(regexpr("[\\.CEL^]", dir(), fixed=FALSE, ignore.case=TRUE))
#rawData <- read.celfiles( regexpr("[\\.CEL^]", dir(), fixed=FALSE, ignore.case=TRUE) )
celFiles <- list.celfiles()
print(celFiles)
rawData <- read.celfiles( grep("[\\.CEL^]$", dir(), fixed=FALSE, ignore.case=TRUE,value=TRUE) )#modified line
} else {
if(exists("prefOligo")) {
if(prefOligo){
require("oligo") #asklars
celFiles <- list.celfiles()
print(celFiles)
try(rawData <- read.celfiles( grep("[\\.CEL^]$", dir(), fixed=FALSE, ignore.case=TRUE,value=TRUE) ),TRUE) #modified line
}
}
if(!exists("rawData")) {
print("reading affy with regular lib")
rawData <- ReadAffy()
} else {
print("data read with oligo")
}
}
##--
print("Raw data have been loaded in R")
}
if(!exists("libdir")) { # libdir exists only for GenePattern usage
setwd(SCRIPT.DIR)
setwd(WORK.DIR)
}
# Make sure that the CDF environment works
if(!isOligo){
rawData <- addStandardCDFenv(rawData) # if already works, won't be changed
# Verify the array type (PMMM or PMonly)
aType <- getArrayType(rawData)
} else {
aType <- "PMonly"
}
# When refName does not exist, use the empty string
if(!exists("refName")) refName <- ""
###############################################################################
# Create array groups and array names #
###############################################################################
if(arrayGroup!=""){
# Information is available: groups will be created
# 1- read the arrayGroup file and trim spaces
# 2- define the array names and classes (experimentFactor)
if(!exists("DESC.DIR")) DESC.DIR <- ""
descfile <- paste(DESC.DIR, arrayGroup, sep="")
extension<-strsplit(descfile,"\\.")
extension<-paste(".",extension[[1]][length(extension[[1]])],sep="")
description = NULL;
switch(extension,
".txt" = description<-as.data.frame(apply(read.delim(descfile, fill = FALSE, as.is=TRUE),2,trimws)),
".csv" = description<-as.data.frame(apply(read.csv(descfile, fill = FALSE, as.is=TRUE),2,trimws)),
".xls" = {library(gdata); description<-as.data.frame(apply(read.xls(descfile, as.is=TRUE),2,trimws))},
".xlsx" = {library(gdata); description<-as.data.frame(apply(read.xls(descfile, as.is=TRUE),2,trimws))}
)
if(is.null(description)) stop(paste("extension",extension,"not recognised"))
# description <- trim(read.table(paste(DESC.DIR, arrayGroup, sep=""),
# header = TRUE, as.is = TRUE, sep="\t"))
if(length(grep(".CEL",toupper(colnames(description)[1]),
ignore.case = TRUE))>0) {
stop(paste("The description file may not contain a header, as the first",
"column header seems to be a CEL file name"))
}
file_order <- match(description[,1],sampleNames(rawData))
if(sum(is.na(file_order)) > 0) stop("file names in data directory and file names in description file do not match")
if(length(unique(file_order)) < length(file_order)) stop("file names in description file are not unique")
rawData <- rawData[,file_order]
sampleNames(rawData)<- as.character(description[,2])
experimentFactor <- factor(description[,3])
# if required reorder the arrays according to group levels in order to keep
# groups together in all plots
if(reOrder) {
rawData <- rawData[,order(experimentFactor)]
experimentFactor <- experimentFactor[order(experimentFactor)]
}
} else {
# No information: arrays will be computed/colored independently
sampleNames(rawData) <- as.character(sampleNames(rawData))
experimentFactor <- factor(rep(1, length(sampleNames(rawData))))
description <- cbind(sampleNames(rawData),sampleNames(rawData),
experimentFactor)
colnames(description) <- c("ArrayDataFile","SourceName","FactorValue")
}
# Create colorset for the array groups
#-------------------------------------
colList <- colorsByFactor(experimentFactor)
plotColors <- colList$plotColors
legendColors <- colList$legendColors
rm(colList)
# Create symbolset for the array groups
#--------------------------------------
plotSymbols <- 18-as.numeric(experimentFactor)
legendSymbols <- sort(plotSymbols, decreasing=TRUE)
###############################################################################
# Define display parameters for the images #
###############################################################################
WIDTH <- 1000
HEIGHT <- 1414
POINTSIZE <- 24
if(!exists("maxArray")) maxArray <- 41
###############################################################################
# Calculate the indicator values and begin the report #
###############################################################################
#create a cover sheet for the report to be created later
#and create a page indicating the naming and grouping used
coverAndKeyPlot(description, refName,WIDTH=WIDTH,HEIGHT=HEIGHT)
#create a table with several QC indicators
if(samplePrep || ratio || hybrid || percPres || bgPlot || scaleFact) {
# The indicators are calculated only for PM-MM arrays as the calculation
# based on MAS5 does not work for PM-only arrays
quality <- NULL
try(quality <- qc(rawData),TRUE) # calculate Affymetrix quality data for PMMM
if(is.null(quality)) {
warning("Plots based on the simpleaffy qc function cannot be created for this chip type")
}
if(samplePrep) {
# find the data
try(yack <- yaqc(rawData),TRUE)
if(exists("yack")) {
spnames<-rownames(yack@morespikes[grep("(lys|phe|thr|dap).*3", # only 3'
rownames(yack@morespikes), ignore.case = TRUE),])
sprep<-t(yack@morespikes[spnames,])
} else {
sprep <- NULL
warning("Plots based on the yaqc function cannot be created for this chip type")
}
try({calls<-detection.p.val(rawData)$call
lys<-calls[rownames(calls)[grep("lys.*3",rownames(calls),ignore.case=TRUE)],]
rm(calls)},TRUE)
if(!exists("lys")) {
lys <- NULL
warning("Plots based on the detection.p.val function cannot be created for this chip type")
}else{
if(length(lys) > length(sampleNames(rawData))) { lys<-lys[1,] }
}
}
QCtablePlot(rawData,quality,sprep,lys,samplePrep=samplePrep,ratio=ratio,
hybrid=hybrid,percPres=percPres,bgPlot=bgPlot,scaleFact=scaleFact,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE)
}
###############################################################################
# Raw data Quality Control graphs #
###############################################################################
print("Graphs ready to be computed")
# 1.1 Sample prep controls
#-------------------------
if(samplePrep && !is.null(sprep) && !is.null(lys)) {
print (" plot sample prep controls" )
samplePrepPlot(rawData,sprep,lys,plotColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
# 1.2 3'/5' ratio - only for PM-MM arrays
#----------------------------------------
if(ratio && !is.null(quality)) {
print (" plot beta-actin & GAPDH 3'/5' ratio")
ratioPlot(rawData,quality=quality,experimentFactor,plotColors,legendColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
# 1.3 RNA degradation plot
#-------------------------
if(degPlot) {
print (" plot degradation plot (skipped for oligo based analysis)" )
try(RNAdegPlot(rawData,plotColors=plotColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray),TRUE)
}
###############################################################################
# 2.1 Spike-in controls - only for PM-MM arrays
#----------------------------------------------
if(hybrid && !is.null(quality)) {
print (" plot spike-in hybridization controls" )
hybridPlot(rawData,quality=quality,plotColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
# 2.2 Background intensities - only for PM-MM arrays
#---------------------------------------------------
if(bgPlot && !is.null(quality)) {
print (" plot background intensities" )
backgroundPlot(rawData,quality=quality,experimentFactor,plotColors,legendColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
# 2.3 Percent present - only for PM-MM arrays
#---------------------------------------------
if(percPres && !is.null(quality)) {
print (" plot percent present" )
percPresPlot(rawData,quality=quality,experimentFactor,plotColors,legendColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
# 2.4 Table of PMA-calls based on the MAS5 algorithm - only for PM-MM arrays
#---------------------------------------------------------------------------
if(PMAcalls) {
if(customCDF) {
if(species=="") {
warning("Species has not been set and custom cdf requested, attempting to deduce species for chip type")
species <- deduceSpecies(rawData@annotation)
}
if(species!=""){
PMAtable <- computePMAtable(rawData,customCDF,species,CDFtype)
}else{
warning("Could not define species; the CDF will not be changed")
PMAtable <- computePMAtable(rawData,customCDF)
}
} else {
PMAtable <- computePMAtable(rawData,customCDF)
}
if(!is.null(PMAtable)) {
write.table(PMAtable, "PMAtable.txt", sep="\t", row.names=FALSE,
col.names=TRUE, quote=FALSE)
}
}
# 2.5 Pos and Neg control distribution
#-------------------------------------
if(posnegDistrib) {
print (" plot pos & neg control distribution (skipped for oligo based analysis)" )
try(PNdistrPlot(rawData,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE),TRUE)
}
# 2.6 affx control profiles and boxplot
#--------------------------------------
if(controlPlot) {
print (" plot control profiles and/or boxplots (skipped for oligo based analysis)")
try(controlPlots(rawData,plotColors,experimentFactor,legendColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray),TRUE)
}
###############################################################################
# 3.1.1 Scale factor - only for PM-MM arrays
#-------------------------------------------
if(scaleFact && !is.null(quality)) {
print (" plot scale factors")
scaleFactPlot(rawData,quality=quality,experimentFactor,plotColors,
legendColors,WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,
MAXARRAY=maxArray)
}
# 3.1.2 Boxplot of raw log-intensities
#-------------------------------------
if(boxplotRaw){
print (" plot boxplot for raw intensities")
boxplotFun(Data=rawData, experimentFactor, plotColors, legendColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
# 3.1.3 Density histogram of raw log-intensities
#-----------------------------------------------
if(densityRaw){
print (" plot density histogram for raw intensities")
densityFun(Data=rawData, plotColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
#densityFunUnsmoothed(Data=rawData, plotColors,
# WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
# 3.2.1 MA-plot or raw data
#--------------------------
if(MARaw){
print (" MA-plots for raw intensities")
maFun(Data=rawData, experimentFactor, perGroup=(MAOption1=="group"),
aType=aType,WIDTH=WIDTH,HEIGHT=HEIGHT,MAXARRAY=maxArray)
}
# 3.3.1 Plot of the array layout
#-------------------------------
if(layoutPlot) {
print (" plot array reference layout")
plotArrayLayout(rawData,aType,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE)
}
# 3.3.2 Pos and Neg control Position
#-----------------------------------
if(posnegCOI && !isOligo){
print (" Pos/Neg COI")
PNposPlot(rawData,WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE)
}
if(!isOligo){ #start of !isOligo
# 3.3.3.1 Create PLM object
#--------------------------
# fit a probe level model on the raw data, used by nuse and rle plot as well
rawData.pset <- NULL
if(spatialImage || PLMimage || Nuse || Rle) {
print (" Fit a probe level model (PLM) on the raw data")
rawData.pset <- fitPLM(rawData)
}
# 3.3.3.2 Spatial images
#---------------------
if(spatialImage) {
print (" 2D virtual images")
valtry<-try(spatialImages(rawData, Data.pset=rawData.pset, TRUE,FALSE,FALSE,FALSE,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE),
silent=TRUE)
if(class(valtry)=="try-error") {
print(" Use array.image instead of spatialImages function")
if(length(sampleNames(rawData))>6){
# Usage of a median array is interesting when there are enough arrays
array.image(rawData,WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE)
}else{
# Usage when few arrays in dataset (one page for 3 arrays -> max: 2 pages)
array.image(rawData,relative=FALSE,col.mod=4,symm=TRUE,WIDTH=WIDTH,
HEIGHT=HEIGHT,POINTSIZE=POINTSIZE)
}
}
}
# 3.3.3.3 PLM images
#---------------------
if(PLMimage) {
print (" Complete set of 2D PLM images")
valtry<-try(spatialImages(rawData, Data.pset=rawData.pset, TRUE, TRUE, TRUE, TRUE,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray),
silent=TRUE)
if(class(valtry)=="try-error") {
print(" Could not create the PLM images.")
}
}
# 3.4.1 NUSE
#-----------
if(Nuse){
print (" NUSE boxplot")
nuseFun(rawData, Data.pset=rawData.pset, experimentFactor, plotColors,
legendColors,WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,
MAXARRAY=maxArray)
}
# 3.4.2 RLE
#----------
if(Rle){
print (" RLE boxplot")
rleFun(rawData, Data.pset=rawData.pset, experimentFactor, plotColors,
legendColors,WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,
MAXARRAY=maxArray)
}
} #end of isOligo
###############################################################################
# 4.1 Correlation Plot of raw data
#----------------------------------
if(correlRaw){
print (" Correlation plot of raw data")
correlFun(Data=rawData, experimentFactor=experimentFactor, legendColors=legendColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
# 4.2 PCA analysis of raw data
#-----------------------------
if(PCARaw){
print(" PCA analysis of raw data")
pcaFun(Data=rawData, experimentFactor=experimentFactor,
plotColors=plotColors, legendColors=legendColors, plotSymbols=plotSymbols,
legendSymbols=legendSymbols, namesInPlot=((max(nchar(sampleNames(rawData)))<=10)&&
(length(sampleNames(rawData))<=(maxArray/2))),WIDTH=WIDTH,HEIGHT=HEIGHT,
POINTSIZE=POINTSIZE)
}
# 4.3 Hierarchical Clustering of raw data
#-----------------------------------------
if(clusterRaw){
print (" Hierarchical clustering of raw data")
clusterFun(Data=rawData, experimentFactor=experimentFactor,
clusterOption1=clusterOption1, clusterOption2=clusterOption2,
plotColors=plotColors, legendColors=legendColors,
plotSymbols=plotSymbols, legendSymbols=legendSymbols,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
###############################################################################
# Pre-processing #
###############################################################################
if (aType == "PMonly") {
if (normMeth == "MAS5") {
warning("MAS5 cannot be applied to PMonly arrays. Changed MAS5 to PLIER")
normMeth <- "PLIER"
}
# if (normMeth == "GCRMA") {
# warning("GCRMA cannot be applied to PMonly arrays. Changed GCRMA to RMA")
# normMeth <- "RMA"
# }
}
if(normMeth!="" && normMeth!="none") {
if(customCDF) {
if(species=="") {
warning("Species has not been set and custom cdf requested, attempting to deduce species for chip type")
species <- deduceSpecies(rawData@annotation)
}
if(species!=""){
normData <- normalizeData(rawData,normMeth,perGroup=(normOption1=="group"),
experimentFactor, aType=aType, customCDF, species, CDFtype, isOligo, WIDTH=WIDTH,
HEIGHT=HEIGHT)
}else{
warning("Could not define species; the CDF will not be changed")
normData <- normalizeData(rawData,normMeth,perGroup=(normOption1=="group"),
experimentFactor, aType=aType, customCDF, isOligo, WIDTH=WIDTH,HEIGHT=HEIGHT)
}
} else {
normData <- normalizeData(rawData,normMeth,perGroup=(normOption1=="group"),
experimentFactor, aType=aType, customCDF,WIDTH=WIDTH,HEIGHT=HEIGHT)
}
}
if((boxplotNorm || densityNorm || MANorm || correlNorm || clusterNorm ||
PCANorm) && ((normMeth=="") || (normMeth=="none"))) {
warning("One or more QC plots of normalized data requested, but no normalization selected, plots will be omitted")
} else {
###############################################################################
# Evaluation of the pre-processing #
###############################################################################
# 5.1 Make a Box-plot of the normalized data
#-------------------------------------------
if(boxplotNorm){
print (" plot boxplot for normalized intensities")
boxplotFun(Data=normData, experimentFactor, plotColors, legendColors,
normMeth=normMeth,WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,
MAXARRAY=maxArray)
}
# 5.2 Make a Density histogram of the normalized data
#----------------------------------------------------
if(densityNorm){
print (" plot density histogram for normalized intensities")
densityFun(Data=normData, plotColors, normMeth=normMeth,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
#densityFunUnsmoothed(Data=normData, plotColors, normMeth=normMeth,
# WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
# 5.3 Make separate MA-plots for each group on normalized data
#-------------------------------------------------------------
if(MANorm){
print (" MA-plots for normalized intensities")
maFun(Data=normData, experimentFactor, perGroup=(MAOption1=="group"),
normMeth=normMeth,WIDTH=WIDTH,HEIGHT=HEIGHT,MAXARRAY=maxArray)
}
# 5.4 Make correlation plots on normalized data
#----------------------------------------------
if(correlNorm){
print (" Correlation plot of normalized data")
correlFun(Data=normData, normMeth=normMeth, experimentFactor=experimentFactor, legendColors=legendColors,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
# 5.5 PCA analysis of normalized data
# -----------------------------------
if(PCANorm){
print(" PCA graph for normalized data")
pcaFun(Data=normData, experimentFactor=experimentFactor,normMeth=normMeth,
plotColors=plotColors, legendColors=legendColors, plotSymbols=plotSymbols,
legendSymbols=legendSymbols, namesInPlot=((max(nchar(sampleNames(rawData)))<=10)&&
(length(sampleNames(rawData))<=(maxArray/2))),WIDTH=WIDTH,HEIGHT=HEIGHT,
POINTSIZE=POINTSIZE)
}
# 5.6 Make hierarchical clustering on normalized data
#----------------------------------------------------
if(clusterNorm){
print (" Hierarchical clustering of normalized data")
clusterFun(Data=normData, experimentFactor=experimentFactor,
clusterOption1=clusterOption1, clusterOption2=clusterOption2,
normMeth=normMeth, plotColors = plotColors, legendColors = legendColors,
plotSymbols=plotSymbols, legendSymbols=legendSymbols,
WIDTH=WIDTH,HEIGHT=HEIGHT,POINTSIZE=POINTSIZE,MAXARRAY=maxArray)
}
}
###############################################################################
# Prepare the output data #
###############################################################################
# Export the normalized data
if((normMeth=="") || (normMeth=="none")) {
warning("No normalization selected, normalized data table not saved")
} else {
print("Saving normalized data table")
if(isOligo)
normDataTable <- createNormDataTable(normData, customCDF=FALSE, species, CDFtype)
else
normDataTable <- createNormDataTable(normData, customCDF=(sum(featureNames(normData)!=featureNames(rawData)[1:length(featureNames(normData))])>0), species, CDFtype)
#output normalised expression data to file
refName <- sub("(_\\d{4}-\\d{2}-\\d{2}_\\d{2}-\\d{2}_\\d{2})", "", refName)
normFileName <- paste(normMeth,"NormData_",refName,".txt",sep="")
print(paste("Normalized data table:", normFileName))
write.table(normDataTable, normFileName, sep="\t", row.names=FALSE, col.names=TRUE, quote=FALSE)
}
# clean R: (or quit without saving the environment...)
# rm(list = ls())
print("I am on test mode")
warning("test mode");
write("prints to stdout", stdout())
if(!is.null(warnings())) warnings()