@@ -1398,12 +1398,13 @@ summarizeNps <- function(strata, index.list, object, batchSize,

 	if(is.lds) {physical <- get("physical"); open(object)}

 	if(verbose) message("      Probe stratum ", strata, " of ", length(index.list))

 	index <- index.list[[strata]]

-	if(CHR.X) {

-		sample.index <- which(object$gender==2)

-		batches <- split(sample.index, as.character(batch(object))[sample.index])

-	} else {

-		batches <- split(seq_along(batch(object)), as.character(batch(object)))

-	}

+##	if(CHR.X) {

+##		sample.index <- which(object$gender==2)

+##		batches <- split(sample.index, as.character(batch(object))[sample.index])

+##	} else {

+##		batches <- split(seq_along(batch(object)), as.character(batch(object)))

+##	}

+	batches <- split(seq_along(batch(object)), as.character(batch(object)))

 	batchnames <- batchNames(object)

 	nr <- length(index)

 	nc <- length(batchnames)

@@ -1418,15 +1419,16 @@ summarizeNps <- function(strata, index.list, object, batchSize,

 		rm(AVG, BB)

 	}

 	for(k in seq_along(batches)){

-		B <- batches[[k]]

-		N.AA[, k] <- length(B)

-		this.batch <- unique(as.character(batch(object)[B]))

+		sample.index <- batches[[k]]

+		N.AA[, k] <- length(sample.index)

+		if(CHR.X){

+			gender <- object$gender[sample.index]

+			sample.index <- sample.index[gender == 2]

+			if(length(sample.index) == 0) next()

+s		}

+		this.batch <- unique(as.character(batch(object)[sample.index]))

 		j <- match(this.batch, batchnames)

-		I.A <- AA[, B]

-##		if(is.illumina){

-##			I.B <- BB[, B]

-##			I.A <- I.A + I.B

-##		}

+		I.A <- AA[, sample.index]

 		medianA.AA[, k] <- rowMedians(I.A, na.rm=TRUE)

 		madA.AA[, k] <- rowMAD(I.A, na.rm=TRUE)

 		## log2 Transform Intensities

@@ -1457,9 +1459,10 @@ summarizeSnps <- function(strata,

 ##	} else {

 ##		batches <- split(seq_along(batch(object)), as.character(batch(object)))

 ##	}

-	if(CHR.X){

-		if(verbose) message("        biallelic cluster medians are estimated using only the women for SNPs on chr. X")

-	}

+	## this message can be confusing if no women are in the dataset

+##	if(CHR.X){

+##		if(verbose) message("        biallelic cluster medians are estimated using only the women for SNPs on chr. X")

+##	}

 	batches <- split(seq_along(batch(object)), as.character(batch(object)))

 	batchnames <- batchNames(object)

 	nr <- length(index)