--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GetNormalizedExpression.R	Mon Jun 16 16:24:48 2014 -0400
@@ -0,0 +1,43 @@
+sink(file="/tmp/none")
+sink("/dev/null")
+options(warn=-1)
+options(echo=F) 
+
+invisible("EBSeq")
+suppressMessages(library("EBSeq"))
+
+args <- commandArgs(trailingOnly = T)
+inputfile <- args[1]
+WhetherSampleName <- args[2]
+outputfile <- args[3]
+Boxplots<-args[4]
+Sizesout <-args[5]
+
+print(args)
+
+if(WhetherSampleName=="y"){
+	ReadIn=read.table(inputfile,stringsAsFactors=F,header=T, sep="\t")
+	Names=names(ReadIn)[-1]
+	}
+if(WhetherSampleName=="n"){
+	ReadIn=read.table(inputfile,stringsAsFactors=F,header=F, sep="\t")
+	Names=paste0("S",1:(length(ReadIn[1,])-1))  ##cms - added 11/11/13
+}
+
+GeneMat=do.call(cbind,ReadIn[-1])
+rownames(GeneMat)=ReadIn[[1]]
+if(WhetherSampleName=="y")colnames(GeneMat)=Names
+if(WhetherSampleName=="n")colnames(GeneMat)=Names  ##cms - added 11/11/13
+
+Sizes=MedianNorm(GeneMat)
+
+Data.norm=GetNormalizedMat(GeneMat, Sizes)
+
+#write.table(round(Data.norm,2),file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
+write.table(round(Data.norm,2),file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t")  ##cms - fixed on 11/11/13
+pdf(Boxplots)
+boxplot(Data.norm,log="y",ylim=c(10^-1,10^6),xlab="Sample",ylab="Normalized Expression")  ##cms - added axis labels on 11/11/13
+dev.off()
+
+write.table(Sizes,file=Sizesout,quote=F,col.names=F,row.names=F,sep = "\t")
+