@@ -326,7 +326,7 @@ C1 <- function(object, marker.index, batch.index, sample.index){

 	return(as.matrix(acn))

 }

-## allele B  (allele 'A' for chromosome X NPs)

+## allele B  (treated allele 'A' for chromosome X NPs)

 ##   autosome SNPs

 ##   chromosome X for male nonpolymorphic markers

 C2 <- function(object, marker.index, batch.index, sample.index, NP.X=FALSE){

@@ -493,9 +493,11 @@ ACN <- function(object, allele, i , j){

 			open(B(object))

 		}

 		if(any(is.auto)){

-			auto.index <- which(is.auto)

-			marker.index <- i[is.auto]

-			acn[auto.index, ] <- C2(object, marker.index, batch.index, j)

+			auto.index <- which(is.auto & is.snp)

+			if(length(auto.index) > 0){

+				marker.index <- i[is.auto]

+				acn[auto.index, ] <- C2(object, marker.index, batch.index, j)

+			}

 		}

 		if(any(is.X)){

 			##Chr X SNPs

@@ -165,14 +165,11 @@ if(!file.exists(file.path(outdir, "cnSet.rda"))){

 			     cdfName=cdfName,

 			     batch=batch)

 	## try normalizing np probes on chr X

-	callSet <- gtSet

-	filenames <- celFiles

-	snp.I <- isSnp(callSet)

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

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

-

-

-

+##	callSet <- gtSet

+##	filenames <- celFiles

+##	snp.I <- isSnp(callSet)

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

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

 }

 @

@@ -253,22 +250,20 @@ ct2 <- totalCopynumber(cnSet, i=marker.index, j=1:5)

 stopifnot(all.equal(ct, ct2))

 @

-Nonpolymorphic markers on X:

-\begin{figure}[!t]

-\centering

-<<nonpolymorphicX>>=

+Nonpolymorphic markers on chromosome X:

+

+\begin{figure}

+  \centering

+<<nonpolymorphicX, fig=TRUE>>=

 npx.index <- which(chromosome(cnSet)==23 & !isSnp(cnSet))

-a <- A(cnSet)[npx.index, M]

-nus <- nuA(cnSet)[npx.index, ]

-## nu and phi are not estimated

 M <- sample(which(cnSet$gender==1), 5)

 F <- sample(which(cnSet$gender==2), 5)

-X.markers <- which(!isSnp(cnSet) & chromosome(cnSet) == 23)

-cn.M <- CA(cnSet, i=X.markers, j=M)

-cn.F <- CA(cnSet, i=X.markers, j=F)

-##phi(cnSet, "A")[X.markers[1:10]]

-index <- which(is.na(nuA(cnSet)[X.markers, 1]))

+##a <- A(cnSet)[npx.index, M]

+##nus <- nuA(cnSet)[npx.index, ]

+## nu and phi are not estimated

+cn.M <- CA(cnSet, i=npx.index, j=M)

+cn.F <- CA(cnSet, i=npx.index, j=F)

 boxplot(data.frame(cbind(cn.M, cn.F)), pch=".")

 @

 \caption{Copy number estimates for nonpolymorphic markers on

@@ -277,13 +272,13 @@ boxplot(data.frame(cbind(cn.M, cn.F)), pch=".")

   males and 2 for females.}

 \end{figure}

-

 Polymorphic markers, X chromosome:

 \begin{figure}

   \centering

 <<polymorphicX, fig=TRUE, width=8, height=4>>=

-X.markers <- sample(which(isSnp(cnSet) & chromosome(cnSet) == 23), 25e3)

+## copy number estimates on X for SNPs are biased towards small values.

+X.markers <- which(isSnp(cnSet) & chromosome(cnSet) == 23)

 ca.M <- CA(cnSet, i=X.markers, j=M)

 cb.M <- CB(cnSet, i=X.markers, j=M)

 ca.F <- CA(cnSet, i=X.markers, j=F)

@@ -294,8 +289,9 @@ boxplot(data.frame(cbind(cn.M, cn.F)), pch=".", outline=FALSE, col=cols, xaxt="n

 legend("topleft", fill=unique(cols), legend=c("Male", "Female"))

 abline(h=c(1,2))

 ## alternatively

-cn.F2 <- totalCopynumber(cnSet, i=X.markers, j=F)

-stopifnot(all.equal(cn.F, cn.F2))

+cn.MF1 <- cbind(cn.M, cn.F)

+cn.MF2 <- totalCopynumber(cnSet, i=X.markers, j=c(M,F))

+##stopifnot(all.equal(cn.MF1[!is.na(cn.MF1)], cn.MF2[!is.na(cn.MF2)]))

 @

 \caption{Copy number estimates for polymorphic markers on chromosome

   X.  We assume that the median copy number (across samples) at any