@@ -733,45 +733,45 @@ crlmmCopynumberLD <- function(object,

 	snpBatches <- splitIndicesByLength(XIndex.snps, ocProbesets())

 	if(verbose) message("Estimating allele-specific copy number at polymorphic loci on chromosome X")

 	ocLapply(seq(along=snpBatches),

-			fit.lm3,

-			marker.index=XIndex.snps,

-			object=object,

-			Ns=Ns,

-			normal=normal,

-			snpflags=snpflags,

-			snpBatches=snpBatches,

-			batchSize=ocProbesets(),

-			SNRMin=SNRMin,

-			MIN.SAMPLES=MIN.SAMPLES,

-			MIN.OBS=MIN.OBS,

-			DF=DF.PRIOR,

-			GT.CONF.THR=GT.CONF.THR,

-			THR.NU.PHI=THR.NU.PHI,

-			MIN.NU=MIN.NU,

-			MIN.PHI=MIN.PHI,

-			verbose=verbose,

+		 fit.lm3,

+		 marker.index=XIndex.snps,

+		 object=object,

+		 Ns=Ns,

+		 normal=normal,

+		 snpflags=snpflags,

+		 snpBatches=snpBatches,

+		 batchSize=ocProbesets(),

+		 SNRMin=SNRMin,

+		 MIN.SAMPLES=MIN.SAMPLES,

+		 MIN.OBS=MIN.OBS,

+		 DF=DF.PRIOR,

+		 GT.CONF.THR=GT.CONF.THR,

+		 THR.NU.PHI=THR.NU.PHI,

+		 MIN.NU=MIN.NU,

+		 MIN.PHI=MIN.PHI,

+		 verbose=verbose,

 		 neededPkgs="crlmm")

 	if(verbose) message("Estimating total copy number for nonpolymorphic loci on chromosome X")

 	snpBatches <- splitIndicesByLength(XIndex.nps, ocProbesets())

-	tmp <- ocLapply(seq(along=snpBatches),

-			fit.lm4,

-			marker.index=XIndex.nps,

-			object=object,

-			Ns=Ns,

-			normal=normal,

-			snpflags=snpflags,

-			snpBatches=snpBatches,

-			batchSize=ocProbesets(),

-			SNRMin=SNRMin,

-			MIN.SAMPLES=MIN.SAMPLES,

-			MIN.OBS=MIN.OBS,

-			DF=DF.PRIOR,

-			GT.CONF.THR=GT.CONF.THR,

-			THR.NU.PHI=THR.NU.PHI,

-			MIN.NU=MIN.NU,

-			MIN.PHI=MIN.PHI,

-			verbose=verbose,

-			neededPkgs="crlmm")

+	ocLapply(seq(along=snpBatches),

+		 fit.lm4,

+		 marker.index=XIndex.nps,

+		 object=object,

+		 Ns=Ns,

+		 normal=normal,

+		 snpflags=snpflags,

+		 snpBatches=snpBatches,

+		 batchSize=ocProbesets(),

+		 SNRMin=SNRMin,

+		 MIN.SAMPLES=MIN.SAMPLES,

+		 MIN.OBS=MIN.OBS,

+		 DF=DF.PRIOR,

+		 GT.CONF.THR=GT.CONF.THR,

+		 THR.NU.PHI=THR.NU.PHI,

+		 MIN.NU=MIN.NU,

+		 MIN.PHI=MIN.PHI,

+		 verbose=verbose,

+		 neededPkgs="crlmm")

 	return(object)

 }

 crlmmCopynumber2 <- crlmmCopynumberLD

@@ -1248,12 +1248,12 @@ fit.lm3 <- function(idxBatch,

 		YA <- muA*wA

 		YB <- muB*wB

 		##res <- nuphiAlleleX(allele="A", Ystar=YA, W=wA)

-		betas <- fit.wls(allele="A", Ystar=YA, W=wA, autosome=FALSE)

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

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

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

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

 		rm(betas)

-		betas <- fit.wls(allele="B", Ystar=YB, W=wB, autosome=FALSE)

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

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

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

 		phiB2[, J] <- betas[3, ]