@@ -323,7 +323,7 @@ C1 <- function(object, marker.index, batch.index, sample.index){

 	if(length(acn) > 1){

 		acn <- do.call("cbind", acn)

 	} else acn <- acn[[1]]

-	return(acn)

+	return(as.matrix(acn))

 }

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

@@ -344,7 +344,7 @@ C2 <- function(object, marker.index, batch.index, sample.index, NP.X=FALSE){

 	if(length(acn) > 1){

 		acn <- do.call("cbind", acn)

 	} else acn <- acn[[1]]

-	return(acn)

+	return(as.matrix(acn))

 }

 ## Chromosome X SNPs

@@ -382,7 +382,7 @@ C3 <- function(object, allele, marker.index, batch.index, sample.index){

 	if(length(acn) > 1){

 		acn <- do.call("cbind", acn)

 	} else acn <- acn[[1]]

-	return(acn)

+	return(as.matrix(acn))

 }

@@ -390,7 +390,7 @@ C3 <- function(object, allele, marker.index, batch.index, sample.index){

 ACN <- function(object, allele, i , j){

 	if(missing(i) & missing(j)) stop("must specify rows (i) or columns (j)")

-	is.ff <- is(calls(object), "ff")

+	is.ff <- is(calls(object), "ff") | is(calls(object), "ffdf")

 	missing.i <- missing(i)

 	missing.j <- missing(j)

 	if(!missing.i){