@@ -46,6 +46,7 @@ getFeatureData <- function(cdfName, copynumber=FALSE){

 		M[index, "chromosome"] <- chromosome2integer(cnProbes[, grep("chr", colnames(cnProbes))])

 		M[index, "isSnp"] <- 0L

 	}

+	##A few of the snpProbes do not match -- I think it is chromosome Y.

 	M <- M[!is.na(M[, "chromosome"]), ]

 	M <- data.frame(M)

 	return(new("AnnotatedDataFrame", data=M))

@@ -145,6 +146,13 @@ genotype <- function(filenames,

 	##message("Saving snprmaRes file")

 	##save(snprmaRes, file=file.path(outdir, "snprmaRes.rda"))

 	if(verbose) message("Finished preprocessing.")

+	gns <- snprmaRes[["gns"]]

+	snp.I <- isSnp(callSet)

+	is.snp <- which(snp.I)

+	snp.index <- match(featureNames(callSet)[is.snp], gns)

+	stopifnot(identical(featureNames(callSet)[is.snp], gns[snp.index]))

+	if(is.lds) open(callSet)

+	mixtureParams <- matrix(NA, 4, length(filenames))

 	if(is.lds){

 		open(snprmaRes[["A"]])

 		open(snprmaRes[["B"]])

@@ -155,24 +163,15 @@ genotype <- function(filenames,

 			   BATCHBYTES=bb)

 		ffcolapply(B(callSet)[is.snp, i1:i2] <- snprmaRes[["B"]][snp.index, i1:i2], X=snprmaRes[["B"]],

 			   BATCHBYTES=bb)

-##		##bb <- getOption("ffbatchbytes")

-##		message("Writing normalized intensities to callSet")

-##		system.time(

-##		for(j in 1:ncol(callSet)){

-##			A(callSet)[is.snp, j] <- snprmaRes[["A"]][snp.index, j]

-##			B(callSet)[is.snp, j] <- snprmaRes[["B"]][snp.index, j]

-##		})

-		##ffrowapply(A(callSet)[i1:i2, ] <- snprmaRes[["A"]][i1:i2, ], X=snprmaRes[["A"]])##, BATCHBYTES=bb)

-		##ffrowapply(B(callSet)[i1:i2, ] <- snprmaRes[["B"]][i1:i2, ], X=snprmaRes[["B"]])##, BATCHBYTES=bb)

-		pData(callSet)$SKW <- snprmaRes[["SKW"]]

-		pData(callSet)$SNR <- snprmaRes[["SNR"]]

 	} else{

 		A(callSet)[is.snp, ] <- snprmaRes[["A"]][snp.index, ]

 		B(callSet)[is.snp, ] <- snprmaRes[["B"]][snp.index, ]

-		pData(callSet)$SKW <- snprmaRes[["SKW"]]

-		pData(callSet)$SNR <- snprmaRes[["SNR"]]

 	}

-	np.index <- which(!snp.I)

+	pData(callSet)$SKW <- snprmaRes[["SKW"]]

+	pData(callSet)$SNR <- snprmaRes[["SNR"]]

+	mixtureParams <- snprmaRes$mixtureParams

+	np.index <- which(!is.snp)

+	if(verbose) message("Normalizing nonpolymorphic markers")

 	FUN <- ifelse(is.lds, "cnrma2", "cnrma")

 	## main purpose is to update 'alleleA'

 	cnrmaFxn <- function(FUN,...){

@@ -222,18 +221,20 @@ genotype <- function(filenames,

 			   BATCHBYTES=bb)

 		ffcolapply(snpCallProbability(callSet)[is.snp, i1:i2] <- tmp[["B"]][snp.index, i1:i2], X=tmp[["B"]],

 			   BATCHBYTES=bb)

-##		for(j in 1:ncol(callSet)){

-##			snpCall(callSet)[is.snp, j] <- tmp[["calls"]][snp.index, j]

-##			snpCallProbability(callSet)[is.snp, j] <- tmp[["confs"]][snp.index, j]

-##		}

-		##		ffrowapply(snpCall(callSet)[i1:i2, ] <- tmp[["calls"]][i1:i2, ], X=tmp[["calls"]])#, BATCHBYTES=bb)

-		##		ffrowapply(snpCallProbability(callSet)[i1:i2, ] <- tmp[["confs"]][i1:i2, ], X=tmp[["confs"]])#, BATCHBYTES=bb)

+		close(tmp[["calls"]])

+		close(tmp[["confs"]])

 	} else {

 		calls(callSet)[is.snp, ] <- tmp[["calls"]][snp.index, ]

 		snpCallProbability(callSet)[is.snp, ] <- tmp[["confs"]][snp.index, ]

 	}

 	message("Finished updating.  Cleaning up.")

 	callSet$gender <- tmp$gender

+	if(is.lds){

+		delete(snprmaRes[["A"]])

+		delete(snprmaRes[["B"]])

+		delete(snprmaRes[["mixtureParams"]])

+		rm(snprmaRes)

+	}

 	close(callSet)

 	if(is.lds){

 		delete(snprmaRes[["A"]])

@@ -936,13 +937,11 @@ fit.lm4 <- function(strata,

 		Y <- log2(c(tmp[, 3], tmp[, 4]))

 		betahat <- solve(crossprod(X), crossprod(X, Y))

 		if(enough.men){

-			##X.men <- cbind(1, medianA.AA.M[, k])

 			X.men <- cbind(1, log2(medianA.AA.M[, k]))

 			Yhat1 <- as.numeric(X.men %*% betahat)

 			## put intercept and slope for men in nuB and phiB

 			phiB[, k] <- 2^(Yhat1)

-			##nuB[, k] <- 2^(medianA.AA.M[, k]) - phiB[, k]

-			nuB[, k] <- medianA.AA.M[, k] - 1*phiB[, k] ## male has 1 copy

+			nuB[, k] <- medianA.AA.M[, k] - 1*phiB[, k]

 		}

 		X.fem <- cbind(1, log2(medianA.AA.F[, k]))

 		Yhat2 <- as.numeric(X.fem %*% betahat)