@@ -421,6 +421,14 @@ setMethod(

   if (is.null(batch)) {

     batch <- rep("all_cells", nC)

+    # If batch null, bgBatch has to be null

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

+      stop(

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

+        "also default to no batch."

+      )

+    }

+

     if (!is.null(countsBackground)) {

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

     }

@@ -15,6 +15,7 @@ decontX(x, ...)

   batch = NULL,

   background = NULL,

   bgAssayName = NULL,

+  bgBatch = NULL,

   maxIter = 500,

   delta = c(10, 10),

   estimateDelta = TRUE,

@@ -32,6 +33,7 @@ decontX(x, ...)

   z = NULL,

   batch = NULL,

   background = NULL,

+  bgBatch = NULL,

   maxIter = 500,

   delta = c(10, 10),

   estimateDelta = TRUE,

@@ -72,15 +74,20 @@ should be considered different batches. Default NULL.}

 \item{background}{A numeric matrix of counts or a

 \linkS4class{SingleCellExperiment} with the matrix located in the assay

-slot under \code{assayName}. It should have the same structure as \code{x}

-except it contains the matrix of empty droplets instead of cells. When

-supplied, empirical distribution of transcripts from these empty droplets

+slot under \code{assayName}. It should have the same data format as \code{x}

+except it contains the empty droplets instead of cells. When supplied, 

+empirical distribution of transcripts from these empty droplets

 will be used as the contamination distribution. Default NULL.}

 \item{bgAssayName}{Character. Name of the assay to use if \code{background}

 is a \linkS4class{SingleCellExperiment}. Default to same as

 \code{assayName}.}

+\item{bgBatch}{Numeric or character vector. Batch labels for 

+\code{background}. Its unique values should be the same as those in

+\code{batch}, such that each batch of cells have their corresponding batch

+of empty droplets as background, pointed by this parameter. Default to NULL.}

+

 \item{maxIter}{Integer. Maximum iterations of the EM algorithm. Default 500.}

 \item{delta}{Numeric Vector of length 2. Concentration parameters for