@@ -424,7 +424,7 @@ setMethod(

     # If batch null, bgBatch has to be null

     if (!is.null(batchBackground)){

       stop(

-        "When experiment default to no bacth, background should",

+        "When experiment default to no bacth, background should ",

         "also default to no batch."

       )

     }

@@ -432,6 +432,17 @@ setMethod(

     if (!is.null(countsBackground)) {

       batchBackground <- rep("all_cells", ncol(countsBackground))

     }

+  } else {

+

+    # If batch not null and countsBackground supplied,

+    # user has to supply batchBackground as well

+    if (!is.null(countsBackground) & is.null(batchBackground)){

+      stop(

+        "Cell batch, and background are supplied. Please also ",

+        "supply background batch."

+      )

+    }

+

   }

   runParams$batch <- batch

   runParams$batchBackground <- batchBackground