@@ -171,7 +171,7 @@ genotype <- function(filenames,

 		       seed=seed,

 		       verbose=verbose)

 	if(verbose) message("Saving callSet.rda")

-	save(callSet, file=file.path(outdir, "callSet.rda"))

+	##save(callSet, file=file.path(outdir, "callSet.rda"))

 	if(!is.lds) A(callSet) <- AA

 	## otherwise, the normalized values were written to file... no need to do anything

 	rm(AA)

@@ -901,12 +901,13 @@ fit.lm4 <- function(strata,

 		X <- cbind(1, log2(c(tmp[, 1], tmp[, 2])))

 		Y <- log2(c(tmp[, 3], tmp[, 4]))

 		betahat <- solve(crossprod(X), crossprod(X, Y))

-		X.men <- cbind(1, medianA.AA.M[, k])

-		Yhat1 <- as.numeric(X.men %*% betahat)

-		## put intercept and slope for men in nuB and phiB

-		phiB[, k] <- 2^(Yhat1)

-		nuB[, k] <- 2^(medianA.AA.M[, k]) - phiB[, k]

-

+		if(enough.men){

+			X.men <- cbind(1, medianA.AA.M[, k])

+			Yhat1 <- as.numeric(X.men %*% betahat)

+			## put intercept and slope for men in nuB and phiB

+			phiB[, k] <- 2^(Yhat1)

+			nuB[, k] <- 2^(medianA.AA.M[, k]) - phiB[, k]

+		}

 		X.fem <- cbind(1, medianA.AA.F[, k])

 		Yhat2 <- as.numeric(X.fem %*% betahat)

 		phiA[, k] <- 2^(Yhat2)

@@ -1492,7 +1493,8 @@ shrinkSummary <- function(object,

 	if(type[[1]] == "X.SNP"){

 		gender <- object$gender

 		if(sum(gender == 2) < 3) {

-			return("too few females to estimate within genotype summary statistics on CHR X")

+			message("too few females to estimate within genotype summary statistics on CHR X")

+			return(object)

 		}

 		CHR.X <- TRUE

 	} else CHR.X <- FALSE

@@ -1540,7 +1542,8 @@ genotypeSummary <- function(object,

 	if(type == "X.SNP" | type=="X.NP"){

 		gender <- object$gender

 		if(sum(gender == 2) < 3) {

-			return("too few females to estimate within genotype summary statistics on CHR X")

+			message("too few females to estimate within genotype summary statistics on CHR X")

+			return(object)

 		}

 		CHR.X <- TRUE

 	} else CHR.X <- FALSE