@@ -546,7 +546,7 @@ setMethod(

     .logMessages(

       date(),

-      ".. Converting decontaminated matrix to ", class(counts),

+      ".. Converting decontaminated matrix to", class(counts),

       logfile = logfile,

       append = TRUE,

       verbose = verbose

@@ -1372,14 +1372,16 @@ simulateContamination <- function(C = 300,

   if (any(dupBarcode)) {

     .logMessages(

+      date(),

+      ".. ",

       sum(dupBarcode),

-      " columns in the background matrix were removed as they were found in",

+      " cells in the background matrix were removed as they were found in",

       " the filtered matrix.",

       logfile = logfile,

       append = TRUE,

       verbose = verbose

     )

-    background <- background[, !(dupBarcode)]

+    background <- background[, !(dupBarcode), drop = FALSE]

   }

   return(background)

 }