@@ -776,7 +776,7 @@ fit.lm3 <- function(strata,

 		madB.Mlist <- res[["madB"]]

 		medianA.Mlist <- res[["medianA"]]

 		medianB.Mlist <- res[["medianB"]]

-		NN.Mlist <- res[["NN.M"]]

+		NN.Mlist <- res[["NN"]]

 		rm(res)

 		## Need N, median, mad

 	}

@@ -791,26 +791,17 @@ fit.lm3 <- function(strata,

 						 is.lds=is.lds,

 						 DF.PRIOR=DF.PRIOR/2,

 					   gender="female")

-		N.AA.F <- as.matrix(N.AA(object)[marker.index, ])

-		N.AB.F <- as.matrix(N.AB(object)[marker.index, ])

-		N.BB.F <- as.matrix(N.BB(object)[marker.index, ])

-		medianA.AA <- as.matrix(medianA.AA(object)[marker.index,])

-		medianA.AB <- as.matrix(medianA.AB(object)[marker.index,])

-		medianA.BB <- as.matrix(medianA.BB(object)[marker.index,])

-		medianB.AA <- as.matrix(medianB.AA(object)[marker.index,])

-		medianB.AB <- as.matrix(medianB.AB(object)[marker.index,])

-		medianB.BB <- as.matrix(medianB.BB(object)[marker.index,])

-		madA.AA <- as.matrix(madA.AA(object)[marker.index,])

-		madA.AB <- as.matrix(madA.AB(object)[marker.index,])

-		madA.BB <- as.matrix(madA.BB(object)[marker.index,])

-		madB.AA <- as.matrix(madB.AA(object)[marker.index,])

-		madB.AB <- as.matrix(madB.AB(object)[marker.index,])

-		madB.BB <- as.matrix(madB.BB(object)[marker.index,])

+		madA.Flist <- res[["madA"]]

+		madB.Flist <- res[["madB"]]

+		medianA.Flist <- res[["medianA"]]

+		medianB.Flist <- res[["medianB"]]

+		NN.Flist <- res[["NN"]]

+		rm(res)

 	}

 	for(k in seq_along(batches)){

-		B <- batches[[k]]

-		this.batch <- unique(as.character(batch(object)[B]))

-		gender <- object$gender[B]

+		sample.index <- batches[[k]]

+		this.batch <- unique(as.character(batch(object)[sample.index]))

+		gender <- object$gender[sample.index]

 		enough.men <- sum(gender==1) >= MIN.SAMPLES

 		enough.women <- sum(gender==2) >= MIN.SAMPLES

 		if(!enough.men & !enough.women) {

@@ -818,11 +809,11 @@ fit.lm3 <- function(strata,

 			next()

 		}

 		if(enough.women){

-			medianA.F <- cbind(medianA.AA[, k], medianA.AB[, k], medianA.BB[, k])

-			medianB.F <- cbind(medianB.AA[, k], medianB.AB[, k], medianB.BB[, k])

-			madA.F <- cbind(madA.AA[, k], madA.AB[, k], madA.BB[, k])

-			madB.F <- cbind(madB.AA[, k], madB.AB[, k], madB.BB[, k])

-			NN.F <- cbind(N.AA.F[, k], N.AB.F[, k], N.BB.F[, k])

+			madA.F <- madA.Flist[[k]]

+			madB.F <- madB.Flist[[k]]

+			medianA.F <- medianA.Flist[[k]]

+			medianB.F <- medianB.Flist[[k]]

+			NN.F <- NN.Flist[[k]]

 		}

 		if(enough.men){

 			madA.M <- madA.Mlist[[k]]

@@ -832,18 +823,18 @@ fit.lm3 <- function(strata,

 			NN.M <- NN.Mlist[[k]]

 		}

 		if(enough.men & enough.women){

-			betas <- fit.wls(cbind(NN.M[, c(1,3)], NN.F),

-					 sigma=cbind(madA.M[, c(1,3)], madA.F),

+			betas <- fit.wls(cbind(NN.M, NN.F),

+					 sigma=cbind(madA.M, madA.F),

 					 allele="A",

-					 Y=cbind(medianA.M[, c(1,3)], medianA.F),

+					 Y=cbind(medianA.M, medianA.F),

 					 autosome=FALSE)

 			nuA[, k] <- betas[1, ]

 			phiA[, k] <- betas[2, ]

 			phiA2[, k] <- betas[3, ]

-			betas <- fit.wls(cbind(NN.M[, c(1,3)], NN.F),

-					 sigma=cbind(madB.M[, c(1,3)], madB.F),

+			betas <- fit.wls(cbind(NN.M, NN.F),

+					 sigma=cbind(madB.M, madB.F),

 					 allele="B",

-					 Y=cbind(medianB.M[, c(1,3)], medianB.F),

+					 Y=cbind(medianB.M, medianB.F),

 					 autosome=FALSE)

 			nuB[, k] <- betas[1, ]

 			phiB[, k] <- betas[2, ]