@@ -592,9 +592,11 @@ setMethod("calculateRBaf", signature(object="CNSet"),

 		  r.expected[grBB] <- r.bb[grBB]

 		  index.np <- which(is.np)

-		  a.np <- A(object)[index.np, ]

-		  meds <- rowMedians(a.np, na.rm=TRUE)

-		  r.expected[index.np, ] <- matrix(meds, length(index.np), ncol(a.np))

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

+			  a.np <- A(object)[index.np, J]

+			  meds <- rowMedians(a.np, na.rm=TRUE)

+			  r.expected[index.np, ] <- matrix(meds, length(index.np), ncol(a.np))

+		  }

 		  lrr <- log2(obs.r/r.expected)

 		  dimnames(bf) <- dimnames(lrr) <- dns