@@ -170,7 +170,8 @@ setMethod("decontX", "SingleCellExperiment", function(x,

     # Remove cells with the same ID between x and the background matrix

     background <- .checkBackground(x = x, background = background,

                                    logfile = logfile, verbose = verbose)

-    # Does bgBatch needs to be checked?

+    

+    # TODO: Does bgBatch needs to be checked?

     if (is.null(bgAssayName)) {

       bgAssayName <- assayName

@@ -255,6 +256,9 @@ setMethod("decontX", "ANY", function(x,

     # Remove cells with the same ID between x and the background matrix

     background <- .checkBackground(x = x, background = background,

                                    logfile = logfile, verbose = verbose)

+    

+    # TODO: Does bgBatch needs to be checked?

+    

   }

   .decontX(

@@ -407,9 +411,9 @@ setMethod(

   if (is.null(batch)) {

     batch <- rep("all_cells", nC)

-    # When no batch, batchBackground can have max 1 batch, depending on if

-    # countsBackground supplied

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

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

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

+    }

   }

   runParams$batch <- batch

   batchIndex <- unique(batch)