setValidity("CopyNumberSet", function(object) {
 	##msg <- validMsg(NULL, Biobase:::isValidVersion(object, "CopyNumberSet"))
 	msg <- validMsg(NULL, assayDataValidMembers(assayData(object), c("CA", "CB")))
 	if (is.null(msg)) TRUE else msg
 })

 ##may want to allow thresholding here (... arg)
 setMethod("CA", "CopyNumberSet", function(object, ...) assayData(object)[["CA"]]/100)
 setMethod("CB", "CopyNumberSet", function(object, ...) assayData(object)[["CB"]]/100)

 setReplaceMethod("CA", signature(object="CopyNumberSet", value="matrix"),

 		 function(object, value) assayDataElementReplace(object, "CA", value*100))
 setReplaceMethod("CB", signature(object="CopyNumberSet", value="matrix"),
 		 function(object, value) assayDataElementReplace(object, "CB", value*100))
 
 

 setMethod("batch", "CopyNumberSet", function(object){
 	if("batch" %in% varLabels(object)){
 		result <- object$batch
 	} else {
 		stop("batch not in varLabels of CopyNumberSet")
 	}
 	return(result)
 })

 
 setMethod("copyNumber", "CopyNumberSet", function(object){

 	require(paste(annotation(object), "Crlmm", sep=""), character.only=TRUE) || stop(paste("Annotation package ", annotation(object), "Crlmm not available", sep=""))

 	##ensure that 2 + NA = 2 by replacing NA's with zero

 	##the above results in copy number 0, 1, or 2 depending on the genotype....safer just to drop

 	CA <- CA(object)
 	CB <- CB(object)

 	##nas <- is.na(CA) & is.na(CB)
 	##CA[is.na(CA)] <- 0
 	##CB[is.na(CB)] <- 0

 	CN <- CA + CB

 	##For nonpolymorphic probes, CA is the total copy number
 	CN[cnIndex(object, annotation(object)), ] <- CA(object)[cnIndex(object, annotation(object)), ]

 	##if both CA and CB are NA, report NA

 	##CN[nas] <- NA

 	CN
 })
 

 ##setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){

 ellipse.CopyNumberSet <- function(x, copynumber, ...){
 ##setMethod("ellipse", "CopyNumberSet", function(x, copynumber, ...){

 	##fittedOrder <- unique(sapply(basename(celFiles), function(x) strsplit(x, "_")[[1]][2]))
 	##index <- match(plates, fittedOrder)
 	if(nrow(x) > 1) stop("only 1 snp at a time")

 	##batch <- unique(x$batch)
 	args <- list(...)
 	if(!"batch" %in% names(args)){
 		jj <- match("batch", varLabels(x))
 		if(length(jj) < 1) stop("batch not in varLabels")
 		batch <- unique(pData(x)[, jj])
 	} else{
 		batch <- unique(args$batch)
 	}

 	if(length(batch) > 1) stop("batch variable not unique")
 	nuA <- as.numeric(fData(x)[, match(paste("nuA", batch, sep="_"), fvarLabels(x))])
 	nuB <- as.numeric(fData(x)[, match(paste("nuB", batch, sep="_"), fvarLabels(x))])	
 	phiA <- as.numeric(fData(x)[, match(paste("phiA", batch, sep="_"), fvarLabels(x))])
 	phiB <- as.numeric(fData(x)[, match(paste("phiB", batch, sep="_"), fvarLabels(x))])	
 	tau2A <- as.numeric(fData(x)[, match(paste("tau2A", batch, sep="_"), fvarLabels(x))])
 	tau2B <- as.numeric(fData(x)[, match(paste("tau2B", batch, sep="_"), fvarLabels(x))])
 	sig2A <- as.numeric(fData(x)[, match(paste("sig2A", batch, sep="_"), fvarLabels(x))])
 	sig2B <- as.numeric(fData(x)[, match(paste("sig2B", batch, sep="_"), fvarLabels(x))])
 	corrA.BB <- as.numeric(fData(x)[, match(paste("corrA.BB", batch, sep="_"), fvarLabels(x))])
 	corrB.AA <- as.numeric(fData(x)[, match(paste("corrB.AA", batch, sep="_"), fvarLabels(x))])
 	corr <- as.numeric(fData(x)[, match(paste("corr", batch, sep="_"), fvarLabels(x))])
 	for(CN in copynumber){
 		for(CA in 0:CN){
 			CB <- CN-CA
 			A.scale <- sqrt(tau2A*(CA==0) + sig2A*(CA > 0))
 			B.scale <- sqrt(tau2B*(CB==0) + sig2B*(CB > 0))
 			scale <- c(A.scale, B.scale)
 			if(CA == 0 & CB > 0) rho <- corrA.BB
 			if(CA > 0 & CB == 0) rho <- corrB.AA
 			if(CA > 0 & CB > 0) rho <- corr

 			if(CA == 0 & CB == 0) rho <- 0

 			lines(ellipse(x=rho, centre=c(log2(nuA+CA*phiA),
 					     log2(nuB+CB*phiB)),
 				      scale=scale), ...)
 		}
 	}

 }