@@ -170,6 +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?

+    

     if (is.null(bgAssayName)) {

       bgAssayName <- assayName

     }

@@ -392,7 +394,7 @@ setMethod(

   nC <- ncol(counts)

   allCellNames <- colnames(counts)

-  ## Set up final deconaminated matrix

+  ## Set up final decontaminated matrix

   estRmat <- Matrix::Matrix(

     data = 0,

     ncol = totalCells,

@@ -404,6 +406,9 @@ setMethod(

   ## Generate batch labels if none were supplied

   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))

   }

   runParams$batch <- batch

@@ -439,6 +444,7 @@ setMethod(

     zBat <- NULL

     countsBat <- counts[, batch == bat]

+    bgBat <- countsBackground[, bactchBackgound == bat]

     ## Convert to sparse matrix

     if (!inherits(countsBat, "dgCMatrix")) {

@@ -451,9 +457,9 @@ setMethod(

       )

       countsBat <- methods::as(countsBat, "dgCMatrix")

     }

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

-      if (!inherits(countsBackground, "dgCMatrix")) {

-        countsBackground <- methods::as(countsBackground, "dgCMatrix")

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

+      if (!inherits(bgBat, "dgCMatrix")) {

+        bgBat <- methods::as(bgBat, "dgCMatrix")

       }

     }

@@ -465,7 +471,7 @@ setMethod(

         counts = countsBat,

         z = zBat,

         batch = bat,

-        countsBackground = countsBackground,

+        countsBackground = bgBat,

         maxIter = maxIter,

         delta = delta,

         estimateDelta = estimateDelta,

@@ -484,7 +490,7 @@ setMethod(

           counts = countsBat,

           z = zBat,

           batch = bat,

-          countsBackground = countsBackground,

+          countsBackground = bgBat,

           maxIter = maxIter,

           delta = delta,

           estimateDelta = estimateDelta,