diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 65cda1fb..1e327edc 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -152,9 +152,11 @@ setReplaceMethod("workingDir", "FraserDataSet", function(object, value) {
 #' @rdname fds-methods
 setMethod("strandSpecific", "FraserDataSet", function(object) {
     if(!"strand" %in% colnames(colData(object))){
-        warning("Strand is not specified. Please set the used RNA-seq",
+        if(ncol(object) > 0){
+            warning("Strand is not specified. Please set the used RNA-seq",
                 " protocol by using 'strandSpecific(object) <- c(...)'.",
                 "\n\nWe assume as default a non stranded protocol.")
+        }
         return(rep(0, ncol(object)))
     }
     return(colData(object)$strand)
diff --git a/R/example_functions.R b/R/example_functions.R
index 1ec450d1..99b90f6d 100644
--- a/R/example_functions.R
+++ b/R/example_functions.R
@@ -43,6 +43,9 @@ createTestFraserSettings <- function(workingDir="FRASER_output"){
     # check that NHDF is NA group
     sampleTable[gene=='NHDF', condition:=NA]
     
+    # set strand specificity column in colData
+    sampleTable[, strand := 0L]
+    
     # create FRASER object
     fds <- FraserDataSet(colData=sampleTable, workingDir=workingDir)
 
diff --git a/R/mergeExternalData.R b/R/mergeExternalData.R
index c5f5dc4c..44ba7123 100644
--- a/R/mergeExternalData.R
+++ b/R/mergeExternalData.R
@@ -93,7 +93,7 @@ mergeExternalData <- function(fds, countFiles, sampleIDs, annotation=NULL){
     rownames(annotation) <- annotation[,"sampleID"]
     newColData <- DataFrame(rbind(fill=TRUE,
             as.data.table(colData(fds)),
-            as.data.table(annotation[sampleIDs,])))
+            as.data.table(annotation[sampleIDs,,drop=FALSE])))
     rownames(newColData) <- newColData[,"sampleID"]
 
     #
diff --git a/R/saveHDF5Objects.R b/R/saveHDF5Objects.R
index 37948de4..a7e89bb7 100644
--- a/R/saveHDF5Objects.R
+++ b/R/saveHDF5Objects.R
@@ -70,11 +70,12 @@ loadFraserDataSet <- function(dir, name=NULL, file=NULL, upgrade=FALSE){
     # can be removed later if the full pipeline is rerun
     attributes(fds)$class <- structure("FraserDataSet", package="FRASER")
     
-    # adapt type of strandSpecific if needed (changed from logical to integer)
-    if(is.logical(strandSpecific(fds))){
-        strandSpecific(fds) <- as.integer(strandSpecific(fds))
+    # ensure strandSpecific slot is up-to-date with new vector format
+    if("strandSpecific" %in% slotNames(fds)){
+        strandSpecific(fds) <- slot(fds, "strandSpecific")    
     }
     
+    
     e <- try(assays(fds), silent=TRUE)
     if(is.error(e)){
         if(grepl("DelayedMatrix .* representation .* Please update it ",
diff --git a/inst/extdata/externalCounts/annotation.tsv.gz b/inst/extdata/externalCounts/annotation.tsv.gz
index 780e0359..8e4edb84 100644
Binary files a/inst/extdata/externalCounts/annotation.tsv.gz and b/inst/extdata/externalCounts/annotation.tsv.gz differ