@@ -657,8 +657,7 @@ crlmmCopynumberLD <- function(object,

 			    MIN.NU=2^3,

 			    MIN.PHI=2^3,

 			    THR.NU.PHI=TRUE,

-			    thresholdCopynumber=TRUE,

-			      weighted.lm=TRUE){

+			    thresholdCopynumber=TRUE){

 	stopifnot("batch" %in% varLabels(protocolData(object)))

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

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

@@ -794,8 +793,7 @@ fit.lm1 <- function(idxBatch,

 		    THR.NU.PHI,

 		    MIN.NU,

 		    MIN.PHI,

-		    verbose,

-		    weighted.lm, ...){

+		    verbose,...){

 	if(isPackageLoaded("ff")) physical <- get("physical")

 	if(verbose) message("Probe batch ", idxBatch, " of ", length(snpBatches))

 	snps <- snpBatches[[idxBatch]]

@@ -907,20 +905,18 @@ fit.lm1 <- function(idxBatch,

 		wB <- sqrt(1/vB2)

 		YA <- muA*wA

 		YB <- muB*wB

-		if(weighted.lm){

-			res <- fit.wls(allele="A", Ystar=YA, W=wA, Ns=Ns)

-		} else{

-			if(zzzz==1) message("currently, only weighted least squares (wls) is available... fitting wls")

-			res <- fit.wls(allele="A", Ystar=YA, W=wA, Ns=Ns)			

-		}

+		res <- fit.wls(allele="A", Ystar=YA, W=wA, Ns=Ns)

+##		} else{

+##			if(zzzz==1) message("currently, only weighted least squares (wls) is available... fitting wls")

+##			res <- fit.wls(allele="A", Ystar=YA, W=wA, Ns=Ns)			

+##		}

 		nuA[, J] <- res[[1]]

 		phiA[, J] <- res[[2]]

-		if(weighted.lm){

-			res <- fit.wls(allele="B", Ystar=YB, W=wB, Ns=Ns)

-		} else {

-			if(zzzz==1) message("currently, only weighted least squares (wls) is available... fitting wls")

-			res <- fit.wls(allele="B", Ystar=YB, W=wB, Ns=Ns)			

-		}

+		res <- fit.wls(allele="B", Ystar=YB, W=wB, Ns=Ns)

+##		} else {

+##			if(zzzz==1) message("currently, only weighted least squares (wls) is available... fitting wls")

+##			res <- fit.wls(allele="B", Ystar=YB, W=wB, Ns=Ns)			

+##		}

 		##nuB[, J] <- res[[1]]

 		nuB[, J] <- res[1, ]

 		##phiB[, J] <- res[[2]]

@@ -1006,8 +1002,7 @@ fit.lm2 <- function(idxBatch,

 		    THR.NU.PHI,

 		    MIN.NU,

 		    MIN.PHI,

-		    verbose,

-		    weighted.lm, ...){

+		    verbose,...){

 	physical <- get("physical")

 	if(verbose) message("Probe batch ", idxBatch, " of ", length(snpBatches))

 	snps <- snpBatches[[idxBatch]]

@@ -2815,8 +2810,7 @@ computeCN <- function(object,

 		      MIN.PHI=2^3,

 		      THR.NU.PHI=TRUE,

 		      thresholdCopynumber=TRUE,

-		      type=c("autosome.snps", "autosome.nps", "X.snps", "X.nps"),

-		      weighted.lm=TRUE){

+		      type=c("autosome.snps", "autosome.nps", "X.snps", "X.nps")){

 	stopifnot("batch" %in% varLabels(protocolData(object)))

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

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

@@ -2930,8 +2924,7 @@ computeCN <- function(object,

 		 MIN.NU=MIN.NU,

 		 MIN.PHI=MIN.PHI,

 		 verbose=verbose,

-		 neededPkgs="crlmm",

-		 weighted.lm=weighted.lm)

+		 neededPkgs="crlmm")

 	message("finished")

 	return(obj)

 }

@@ -120,7 +120,7 @@ copy number estimation and, therefore, we do not need to preprocess

 and genotype the files a second time.

 <<genotype>>=

-if(!file.exists(file.path(outdir, "cnSet.rda"))){

+if(!file.exists(file.path(outdir, "cnSet.assayData_matrix.rda"))){

 	gtSet.assayData_matrix <- checkExists("gtSet.assayData_matrix",

 					   .path=outdir,

 					   .FUN=genotype,

@@ -146,10 +146,6 @@ cnSet.assayData_matrix <- checkExists("cnSet.assayData_matrix",

 				      .FUN=crlmmCopynumber,

 				      object=gtSet.assayData_matrix,

 				      chromosome=22)

-##Rprof(interval=0.1)

-obj <- crlmmCopynumber(gtSet.assayData_matrix, chromosome=23)

-if(file.exists(file.path(outdir, "gtSet.assayData_matrix.rda")))

-	unlink(file.path(outdir, "gtSet.assayData_matrix.rda"))

 @ 

@@ -201,13 +197,12 @@ Rprof(filename="Rprof_cnff.out", interval=0.1)

 cnSet.assayData_ff <- checkExists("cnSet.assayData_ff",

 				  .path=outdir,

 				  .FUN=crlmmCopynumberLD,

-				  filenames=celFiles,

-				  cdfName=cdfName,

-				  batch=batch)

+				  object=gtSet.assayData_ff)

 Rprof(NULL)

-if(file.exists(file.path(outdir, "gtSet.assayData_ff.rda")))

-	unlink(file.path(outdir, "gtSet.assayData_ff.rda"))

+##if(file.exists(file.path(outdir, "gtSet.assayData_ff.rda")))

+##	unlink(file.path(outdir, "gtSet.assayData_ff.rda"))

 gc()

+q("no")

 @ 

 The objects returned by the \Rfunction{genotypeLD} and