read.imagene <- function(files,path=NULL,ext=NULL,names=NULL,columns=NULL,other.columns=NULL,wt.fun=NULL,verbose=TRUE,sep="\t",quote="\"",...) {

 #	Extracts an RG list from a series of Imagene analysis output files.
 #	Imagene requires special treatment because red and green channel
 #	intensities are in different files.
 #	Gordon Smyth

 #	14 Aug 2003.  Last modified 30 Dec 2006.

 
 	if(is.null(dim(files))) {
 		if(length(files)%%2==0)
 			files <- matrix(files, ncol=2, byrow=TRUE)
 		else
 			stop("Odd number of files: should be two data files for each array")
 	} else {
 		files <- as.matrix(files)
 		if(ncol(files) != 2) stop("Need a two column matrix of file names")
 	}
 	if(!is.null(ext)) files <- array(paste(files,ext,sep="."),dim(files))
 	narrays <- nrow(files)

 	if(is.null(names)) names <- paste(removeExt(files[,1]),removeExt(files[,2]),sep=".")

 
 #	Read header information from first file to get nspots
 	fullname <- files[1,1]
 	if(!is.null(path)) fullname <- file.path(path,fullname)
 	headers <- readImaGeneHeader(fullname)
 	if(verbose) cat("Read header information\n")
 	skip <- headers$NHeaderRecords

 	FD <- headers$"Field Dimensions"
 	if(is.null(FD)) stop("Can't find Field Dimensions in ImaGene header")

 	nspots <- sum(apply(FD,1,prod))

 #	Set signal and background estimation method
 	if(is.null(columns)) {
 		SM <- headers$"Measurement parameters"$"Segmentation Method"
 		if(is.null(SM)) SM <- "none"
 		if(SM=="auto")
 			columns <- list(f="Signal Mean",b="Background Mean")
 		else
 			columns <- list(f="Signal Mean",b="Background Median")
 	}
 	if(is.null(columns$f) || is.null(columns$b)) stop("'columns' should have components 'f' and 'b'")
 

 #	Initialize data object

 	Y <- matrix(0,nspots,narrays)
 	colnames(Y) <- names

 	RG <- list(R=Y,G=Y,Rb=Y,Gb=Y,source="imagene",Field.Dimensions=FD)

 	if(!is.null(wt.fun)) RG$weights <- Y

 
 #	Other columns
 	if(!is.null(other.columns)) {
 		other.columns <- as.character(other.columns)
 		if(length(other.columns)) {
 			RG$other <- list()
 			G.other.columns <- paste("G",other.columns)
 			colnames(Y) <- removeExt(files[,1])
 			for (a in G.other.columns) RG$other[[a]] <- Y 
 			R.other.columns <- paste("R",other.columns)
 			colnames(Y) <- removeExt(files[,2])
 			for (a in R.other.columns) RG$other[[a]] <- Y 
 		} else {
 			other.columns <- NULL
 		}
 	}
 

 	printer <- list(ngrid.r=FD[1,"Metarows"],ngrid.c=FD[1,"Metacols"],nspot.r=FD[1,"Rows"],nspot.c=FD[1,"Cols"])

 	if(nrow(FD)==1) {

 		RG$printer <- printer
 	} else {
 		printer$ngrid.r <- sum(FD[,"Metarows"])

 		if(all(printer$ngrid.c==FD[,"Metacols"]) &&

 			all(printer$nspot.r==FD[,"Rows"]) &&
 			all(printer$nspot.c==FD[,"Cols"]) ) RG$printer <- printer

 	}

 
 #	Now read data

 	for (i in 1:narrays) {

 
 #		Green channel

 		fullname <- files[i,1]
 		if(!is.null(path)) fullname <- file.path(path,fullname)
 		if(i > 1) {
 			headers <- readImaGeneHeader(fullname)
 			if(any(headers[["Field Dimensions"]] != RG$Field.Dimensions))
 				stop(paste("Field dimensions of array",i,"not same as those of first array"))
 			skip <- headers$NHeaderRecords
 		}
 		obj<- read.table(fullname,skip=skip,header=TRUE,sep=sep,quote=quote,check.names=FALSE,comment.char="",fill=TRUE,nrows=nspots,...)
 		if(verbose) cat(paste("Read",fullname,"\n"))
 		if(i==1) RG$genes <- obj[,c("Field","Meta Row","Meta Column","Row","Column","Gene ID")]
 		RG$G[,i] <- obj[,columns$f]
 		RG$Gb[,i] <- obj[,columns$b]

 		if(!is.null(other.columns)) {
 			for (j in 1:length(other.columns)) RG$other[[G.other.columns[j]]][,i] <- obj[,other.columns[j]]
 		}
 
 #		Red channel		

 		fullname <- files[i,2]
 		if(!is.null(path)) fullname <- file.path(path,fullname)
 		obj<- read.table(fullname,skip=skip,header=TRUE,sep=sep,quote=quote,check.names=FALSE,comment.char="",fill=TRUE,nrows=nspots,...)
 		if(verbose) cat(paste("Read",fullname,"\n"))
 		RG$R[,i] <- obj[,columns$f]
 		RG$Rb[,i] <- obj[,columns$b]
 		if(!is.null(wt.fun)) RG$weights[,i] <- wt.fun(obj)

 		if(!is.null(other.columns)) {
 			for (j in 1:length(other.columns)) RG$other[[R.other.columns[j]]][,i] <- obj[,other.columns[j]]
 		}

 	}
 	new("RGList",RG)
 }