diff --git a/R/SCESet-functions.R b/R/SCE-functions.R
similarity index 100%
rename from R/SCESet-functions.R
rename to R/SCE-functions.R
diff --git a/R/lun-estimate.R b/R/lun-estimate.R
index 89700790559b8f38851d55bfd8fc5b7b04e6ec73..afa303f239980e85ab49a77ce14c672d2602ebb4 100644
--- a/R/lun-estimate.R
+++ b/R/lun-estimate.R
@@ -25,7 +25,7 @@ lunEstimate <- function(counts, params = newLunParams()) {
 #' @rdname lunEstimate
 #' @export
 lunEstimate.SingleCellExperiment <- function(counts, params = newLunParams()) {
-    counts <- SingleCellExperiment::counts(counts)
+    counts <- SummarizedExperiment::assays(counts)$counts
     lunEstimate(counts, params)
 }
 
diff --git a/R/lun2-estimate.R b/R/lun2-estimate.R
index b4786b4f2d5f5aab9d3cf185653adea217402885..33a0d65365afb0351fc0290d6ec2ecf1a2dfe29f 100644
--- a/R/lun2-estimate.R
+++ b/R/lun2-estimate.R
@@ -40,7 +40,7 @@ lun2Estimate.SingleCellExperiment <- function(counts, plates,
                                               params = newLun2Params(),
                                               min.size = 200, verbose = TRUE,
                                               BPPARAM = SerialParam()) {
-    counts <- SingleCellExperiment::counts(counts)
+    counts <- SummarizedExperiment::assays(counts)$counts
     lun2Estimate(counts, plates, params, min.size = min.size, verbose = verbose)
 }
 
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index 5f5215715e3af645d788644e10973b103d48eeb7..5626394be1e73fbc3ab80afc7d806ec09b0cd0c8 100644
--- a/R/scDD-estimate.R
+++ b/R/scDD-estimate.R
@@ -40,7 +40,7 @@ scDDEstimate.SingleCellExperiment <- function(counts, conditions,
                                               params = newSCDDParams(),
                                               verbose = TRUE,
                                               BPPARAM = SerialParam()) {
-    counts <- SingleCellExperiment::counts(counts)
+    counts <- SummarizedExperiment::assays(counts)$counts
     scDDEstimate(counts, conditions, params, verbose, BPPARAM)
 }
 
diff --git a/R/simple-estimate.R b/R/simple-estimate.R
index 793be3c221c0ca428fa4d3ba114ab590e7994c87..4f09ed4b2ae5b72cd4adf68e65300b58d53d4922 100644
--- a/R/simple-estimate.R
+++ b/R/simple-estimate.R
@@ -28,7 +28,7 @@ simpleEstimate <- function(counts, params = newSimpleParams()) {
 #' @export
 simpleEstimate.SingleCellExperiment <- function(counts,
                                                 params = newSimpleParams()) {
-    counts <- SingleCellExperiment::counts(counts)
+    counts <- SummarizedExperiment::assays(counts)$counts
     simpleEstimate(counts, params)
 }
 
diff --git a/R/splat-estimate.R b/R/splat-estimate.R
index b1523f285640a9d29a12afb7236e087cbf67d699..496edf19324b7dae80e02a5a415f43bfdd834d60 100644
--- a/R/splat-estimate.R
+++ b/R/splat-estimate.R
@@ -28,7 +28,7 @@ splatEstimate <- function(counts, params = newSplatParams()) {
 #' @export
 splatEstimate.SingleCellExperiment <- function(counts,
                                                params = newSplatParams()) {
-    counts <- SingleCellExperiment::counts(counts)
+    counts <- SummarizedExperiment::assays(counts)$counts
     splatEstimate(counts, params)
 }