@@ -769,8 +769,8 @@ fit.lm1 <- function(idxBatch,

 		    marker.index,

 		    object,

 		    Ns,

-		    normal,

-		    snpflags,

+##		    normal,

+##		    snpflags,

 		    batchSize,

 		    SNRMin,

 		    MIN.SAMPLES,

@@ -977,8 +977,8 @@ fit.lm2 <- function(idxBatch,

 		    marker.index,

 		    object,

 		    Ns,

-		    normal,

-		    snpflags,

+##		    normal,

+##		    snpflags,

 		    batchSize,

 		    SNRMin,

 		    MIN.SAMPLES,

@@ -1088,8 +1088,8 @@ fit.lm3 <- function(idxBatch,

 		    marker.index,

 		    object,

 		    Ns,

-		    normal,

-		    snpflags,

+##		    normal,

+##		    snpflags,

 		    batchSize,

 		    SNRMin,

 		    MIN.SAMPLES,

@@ -1327,8 +1327,8 @@ fit.lm4 <- function(idxBatch,

 		    marker.index,

 		    object,

 		    Ns,

-		    normal,

-		    snpflags,

+##		    normal,

+##		    snpflags,

 		    batchSize,

 		    SNRMin,

 		    MIN.SAMPLES,

@@ -1442,7 +1442,6 @@ fit.lm4 <- function(idxBatch,

 		if(any(pseudoAR)){

 			nu1[pseudoAR] <- 2^(mus[pseudoAR, 1]) - 2*phi1[pseudoAR]

 		}

-

 ##              normal.f <- NORM.np[, k]

 ##		A.F <- A.F*normal.f[, gend==2]

 		A.F[A.F==0] <- NA

@@ -2774,6 +2773,7 @@ ellipseCenters <- function(object, index, allele, batch, log.it=TRUE){

 	return(centers)

 }

+

 computeCN <- function(object,

 		      filenames,

 		      which.batches,

@@ -2798,89 +2798,44 @@ computeCN <- function(object,

 	stopifnot("position" %in% fvarLabels(object))

 	stopifnot("isSnp" %in% fvarLabels(object))

 	batch <- batch(object)

+	is.snp <- isSnp(object)

+	is.autosome <- chromosome(object) < 23

+	is.annotated <- !is.na(chromosome(object))

+	is.X <- chromosome(object) == 23

 	if(type=="autosome.snps"){

-		marker.index <- which(chromosome(object) < 23 & isSnp(object) & !is.na(chromosome(object)))

+		marker.index <- which(is.snp & is.autosome & is.annotated)

 		nr <- length(marker.index)

 		Ns <- initializeBigMatrix("Ns", nr, 5)

 		colnames(Ns) <- c("A", "B", "AA", "AB", "BB")

-		if(!file.exists(file.path(ldPath(), "normal.snps.rda"))){

-			normal <- initializeBigMatrix("normal.snps", nr, ncol(object), vmode="integer")

-			normal[,] <- 1L

-			save(normal, file=file.path(ldPath(), "normal.snps.rda"))

-		} else load(file.path(ldPath(), "normal.snps.rda"))

-		if(!file.exists(file.path(ldPath(), "flags.snps.rda"))){

-			flags <- initializeBigMatrix("flags.snps", nr, length(unique(batch(object))), vmode="integer")

-			flags[,] <- 0L

-			save(flags, file=file.path(ldPath(), "flags.snps.rda"))

-		} else{

-			load(file.path(ldPath(), "flags.snps.rda"))

-		}

 		if(verbose) message("Estimating allele-specific copy number at autosomal SNPs")

 		FUN <- fit.lm1

 	}

 	if(type=="autosome.nps"){

-		marker.index <- which(chromosome(object) < 23 & !isSnp(object) & !is.na(chromosome(object)))

-		##marker.index <- which(chromosome(object) < 23 & isSnp(object) & !is.na(chromosome(object)))

+		marker.index <- which(is.autosome & !is.snp & is.annotated)

 		nr <- length(marker.index)

 		Ns <- initializeBigMatrix("Ns", nr, 5)

 		colnames(Ns) <- c("A", "B", "AA", "AB", "BB")

-		if(!file.exists(file.path(ldPath(), "normal.snps.rda"))){

-			normal <- initializeBigMatrix("normal.nps", nr, ncol(object), vmode="integer")

-			normal[,] <- 1L

-			save(normal, file=file.path(ldPath(), "normal.nps.rda"))

-		} else load(file.path(ldPath(), "normal.nps.rda"))

-		if(!file.exists(file.path(ldPath(), "flags.nps.rda"))){

-			flags <- initializeBigMatrix("flags.nps", nr, length(unique(batch(object))), vmode="integer")

-			flags[,] <- 0L

-			save(flags, file=file.path(ldPath(), "flags.nps.rda"))

-		} else{

-			load(file.path(ldPath(), "flags.nps.rda"))

-		}

 		if(verbose) message("Estimating allele-specific copy number at autosomal SNPs")

 		FUN <- fit.lm2

 	}

 	if(type=="X.snps"){

-		marker.index <- which(chromosome(object) == 23 & isSnp(object) & !is.na(chromosome(object)))

-		##marker.index <- which(chromosome(object) < 23 & isSnp(object) & !is.na(chromosome(object)))

+		marker.index <- which(is.X & is.snp)

 		nr <- length(marker.index)

 		Ns <- initializeBigMatrix("Ns", nr, 5)

 		colnames(Ns) <- c("A", "B", "AA", "AB", "BB")

-		if(!file.exists(file.path(ldPath(), "normal.X.snps.rda"))){

-			normal <- initializeBigMatrix("normal.X.snps", nr, ncol(object), vmode="integer")

-			normal[,] <- 1L

-			save(normal, file=file.path(ldPath(), "normal.X.snps.rda"))

-		} else load(file.path(ldPath(), "normal.X.snps.rda"))

-		if(!file.exists(file.path(ldPath(), "flags.X.snps.rda"))){

-			flags <- initializeBigMatrix("flags.X.snps", nr, length(unique(batch(object))), vmode="integer")

-			flags[,] <- 0L

-			save(flags, file=file.path(ldPath(), "flags.X.snps.rda"))

-		} else{

-			load(file.path(ldPath(), "flags.X.snps.rda"))

-		}

 		if(verbose) message("Estimating allele-specific copy number at autosomal SNPs")

 		FUN <- fit.lm3

 	}

 	if(type=="X.nps"){

-		marker.index <- which(chromosome(object) == 23 & !isSnp(object) & !is.na(chromosome(object)))

+		marker.index <- which(is.X & !is.snp)

 		nr <- length(marker.index)

 		Ns <- initializeBigMatrix("Ns", nr, 5)

 		colnames(Ns) <- c("A", "B", "AA", "AB", "BB")

-		if(!file.exists(file.path(ldPath(), "normal.X.nps.rda"))){

-			normal <- initializeBigMatrix("normal.X.nps", nr, ncol(object), vmode="integer")

-			normal[,] <- 1L

-			save(normal, file=file.path(ldPath(), "normal.X.nps.rda"))

-		} else load(file.path(ldPath(), "normal.X.nps.rda"))

-		if(!file.exists(file.path(ldPath(), "flags.X.nps.rda"))){

-			flags <- initializeBigMatrix("flags.X.nps", nr, length(unique(batch(object))), vmode="integer")

-			flags[,] <- 0L

-			save(flags, file=file.path(ldPath(), "flags.X.nps.rda"))

-		} else{

-			load(file.path(ldPath(), "flags.X.nps.rda"))

-		}

 		if(verbose) message("Estimating allele-specific copy number at autosomal SNPs")

 		FUN <- fit.lm4

 	}

 	index.strata <- splitIndicesByLength(marker.index, ocProbesets())

+	## create a separate object for each strata and combine() at the very end.

 	obj <- construct(filenames=filenames,

 			 cdfName=annotation(object),

 			 copynumber=TRUE,

@@ -2892,8 +2847,8 @@ computeCN <- function(object,

 		 marker.index=marker.index,

 		 object=obj,

 		 Ns=Ns,

-		 normal=normal,

-		 snpflags=flags,

+		 ##normal=normal,

+		 ##snpflags=flags,

 		 snpBatches=index.strata,

 		 batchSize=ocProbesets(),

 		 SNRMin=SNRMin,