@@ -471,22 +471,16 @@ nuphiAllele <- function(object, allele, Ystar, W, tmp.objects, cnOptions){

 	W <- W[I, ]

 	if(any(!is.finite(W))){## | any(!is.finite(V))){

 		i <- which(rowSums(!is.finite(W)) > 0)

-		##browser()

 		stop("Possible zeros in the within-genotype estimates of the spread (vA, vB). ")

 	}	

 	Ns <- tmp.objects[["Ns"]]	

 	Ns <- Ns[I, ]

 	CHR <- unique(chromosome(object))

-	##batch <- unique(object$batch)

 	batch <- unique(batch(object))

 	nuA <- getParam(object, "nuA", batch)

 	nuB <- getParam(object, "nuB", batch)

-##	nuA.se <- getParam(object, "nuA.se", batch)

-##	nuB.se <- getParam(object, "nuB.se", batch)

 	phiA <- getParam(object, "phiA", batch)

 	phiB <- getParam(object, "phiB", batch)

-##	phiA.se <- getParam(object, "phiA.se", batch)

-##	phiB.se <- getParam(object, "phiB.se", batch)	

 	if(CHR==23){

 		phiAX <- getParam(object, "phiAX", batch)

 		phiBX <- getParam(object, "phiBX", batch)		

@@ -494,7 +488,6 @@ nuphiAllele <- function(object, allele, Ystar, W, tmp.objects, cnOptions){

 	NOHET <- mean(Ns[, "AB"], na.rm=TRUE) < 0.05

 	if(missing(allele)) stop("must specify allele")

 	if(CHR == 23){

-		##Design matrix for X chromosome depends on whether there was a sufficient number of AB genotypes

 		if(length(grep("AB", colnames(W))) > 0){

 			if(allele == "A") X <- cbind(1, c(1, 0, 2, 1, 0), c(0, 1, 0, 1, 2))

 			if(allele == "B") X <- cbind(1, c(0, 1, 0, 1, 2), c(1, 0, 2, 1, 0))

@@ -508,27 +501,16 @@ nuphiAllele <- function(object, allele, Ystar, W, tmp.objects, cnOptions){

 		if(NOHET) X <- X[-2, ] ##more than 1 X chromosome, but all homozygous

 		betahat <- matrix(NA, 2, nrow(Ystar))

 	}

-	##How to quickly generate Xstar, Xstar = diag(W) %*% X

-##	Xstar <- apply(W, 1, generateX, X)

-##	IXTX <- apply(Xstar, 2, generateIXTX, nrow=nrow(X))

-	##as.numeric(diag(W[1, ]) %*% X)

 	ww <- rep(1, ncol(Ystar))

 	II <- which(rowSums(is.nan(Ystar)) == 0)

 	for(i in II){

 		betahat[, i] <- dqrlsWrapper(W[i, ] * X, Ystar[i, ], ww)

-		##betahat[, i] <- crossprod(matrix(IXTX[, i], ncol(X), ncol(X)), crossprod(matrix(Xstar[, i], nrow=nrow(X)), Ystar[i, ]))

-		##ssr <- sum((Ystar[i, ] - matrix(Xstar[, i], nrow(X), ncol(X)) %*% matrix(betahat[, i], ncol(X), 1))^2)

-		##ses[, i] <- sqrt(diag(matrix(IXTX[, i], ncol(X), ncol(X)) * ssr))

 	}

 	if(allele == "A"){

 		nuA[complete] <- betahat[1, ]

 		phiA[complete] <- betahat[2, ]

-##		nuA.se[complete] <- ses[1, ]

-##		phiA.se[complete] <- ses[2, ]

 		object <- pr(object, "nuA", batch, nuA)

-##		object <- pr(object, "nuA.se", batch, nuA.se)

 		object <- pr(object, "phiA", batch, phiA)

-##		object <- pr(object, "phiA.se", batch, phiA.se)

 		if(CHR == 23){

 			phiAX[complete] <- betahat[3, ]

 			object <- pr(object, "phiAX", batch, phiAX)			

@@ -537,23 +519,13 @@ nuphiAllele <- function(object, allele, Ystar, W, tmp.objects, cnOptions){

 	if(allele=="B"){

 		nuB[complete] <- betahat[1, ]

 		phiB[complete] <- betahat[2, ]

-##		nuB.se[complete] <- ses[1, ]

-##		phiB.se[complete] <- ses[2, ]

 		object <- pr(object, "nuB", batch, nuB)

-##		object <- pr(object, "nuB.se", batch, nuB.se)

 		object <- pr(object, "phiB", batch, phiB)		

-##		object <- pr(object, "phiB.se", batch, phiB.se)

 		if(CHR == 23){

 			phiBX[complete] <- betahat[3, ]

 			object <- pr(object, "phiBX", batch, phiBX)

 		}

 	}

-##	THR.NU.PHI <- cnOptions$THR.NU.PHI

-##	if(THR.NU.PHI){

-##		verbose <- cnOptions$verbose

-##		if(verbose) message("Thresholding nu and phi")

-##		object <- thresholdModelParams(object, cnOptions)

-##	}

 	return(object)

 }