@@ -2547,8 +2547,16 @@ numberGenotypes <- function(CT){

 		       tau2B,

 		       sig2A,

 		       sig2B,

+		       nuA,

+		       nuB,

+		       phiA,

+		       phiB,

+		       corrAA,

+		       corrAB,

+		       corrBB,

 		       a,

-		       b){

+		       b,

+		       scale.sd){

 	## 5: AAAAA, AAAAB, AAABB, AABBB, ABBBB, BBBBB

 	##CN=4

 	## AAAA, AAAB, AABB, ABBB, BBBB:  L = 4

@@ -2604,7 +2612,7 @@ posteriorMean.snp <- function(stratum, object, index.list, CN,

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

 	index <- index.list[[stratum]]

 	test <- tryCatch(open(A(object)), error=function(e) NULL)

-	if(!is.null(test)) .open(object)

+	if(!is.null(test)) invisible(.open(object))

 	a <- log2(as.matrix(A(object)[index, ]))

 	b <- log2(as.matrix(B(object)[index, ]))

 	NN <- Ns(object, i=index)[, , 1]

@@ -2619,7 +2627,7 @@ posteriorMean.snp <- function(stratum, object, index.list, CN,

 	phiA <- as.matrix(phiA(object)[index, ])

 	nuB <- as.matrix(nuB(object)[index, ])

 	phiB <- as.matrix(phiB(object)[index, ])

-	if(!is.null(test)) .close(object)

+	if(!is.null(test)) invisible(.close(object))

 	S <- length(prior.prob)

 	emit <- array(NA, dim=c(nrow(a), ncol(a), S))##SNPs x sample x 'truth'

 	sample.index <- split(1:ncol(object), batch(object))

@@ -2630,13 +2638,21 @@ posteriorMean.snp <- function(stratum, object, index.list, CN,

 		probs <- array(NA, dim=c(nrow(a), length(J), S))

 		for(k in seq_along(CN)){

 			##CT <- CN[k]

-			probs[, , k] <- .posterior(CN[k],

-						   tau2A,

-						   tau2B,

-						   sig2A,

-						   sig2B,

-						   a[, J],

-						   b[, J])

+			probs[, , k] <- .posterior(CT=CN[k],

+						   tau2A=tau2A,

+						   tau2B=tau2B,

+						   sig2A=sig2A,

+						   sig2B=sig2B,

+						   nuA=nuA,

+						   nuB=nuB,

+						   phiA=phiA,

+						   phiB=phiB,

+						   corrAA=corrAA,

+						   corrAB=corrAB,

+						   corrBB=corrBB,

+						   a=a[, J],

+						   b=b[, J],

+						   scale.sd=scale.sd)

 			##probs[, , k] <- do.call("sum", f.x.y)

 			##if none of the states are likely (outlier), assign NA

 			##		emit[, , counter] <- f.x.y