diff --git a/R/SCE-functions.R b/R/SCE-functions.R
index a4b97d8cb8ee9ea20cdd4f9600f00229713abf1e..34bc7ad8e81af276a566768f7a7a4f3aacf8da4f 100644
--- a/R/SCE-functions.R
+++ b/R/SCE-functions.R
@@ -33,15 +33,15 @@ addFeatureStats <- function(sce, value = c("counts", "cpm", "tpm", "fpkm"),
 
     switch(value,
            counts = {
-               values = SummarizedExperiment::assays(sce)$counts
+               values = BiocGenerics::counts(sce)
                suffix <- "Counts"
            },
            cpm = {
-               values = SummarizedExperiment::assays(sce)$cpm
+               values = SingleCellExperiment::cpm(sce)
                suffix <- "CPM"
            },
            tpm = {
-               values = SummarizedExperiment::assays(sce)$tpm
+               values = SingleCellExperiment::tpm(sce)
                suffix <- "TPM"
            },
            fpkm = {
diff --git a/R/lun-estimate.R b/R/lun-estimate.R
index afa303f239980e85ab49a77ce14c672d2602ebb4..3191a5d81b2ae16ce8c902f86faf7371830d1ad8 100644
--- a/R/lun-estimate.R
+++ b/R/lun-estimate.R
@@ -25,7 +25,7 @@ lunEstimate <- function(counts, params = newLunParams()) {
 #' @rdname lunEstimate
 #' @export
 lunEstimate.SingleCellExperiment <- function(counts, params = newLunParams()) {
-    counts <- SummarizedExperiment::assays(counts)$counts
+    counts <- BiocGenerics::counts(counts)
     lunEstimate(counts, params)
 }
 
diff --git a/R/lun2-estimate.R b/R/lun2-estimate.R
index 33a0d65365afb0351fc0290d6ec2ecf1a2dfe29f..df51b84699291ace5b99df5da81caefd1d8c88c0 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 <- SummarizedExperiment::assays(counts)$counts
+    counts <- BiocGenerics::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 5626394be1e73fbc3ab80afc7d806ec09b0cd0c8..7253c61e01dda32fbac1cba7c14324fafb05142f 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 <- SummarizedExperiment::assays(counts)$counts
+    counts <- BiocGenerics::counts(counts)
     scDDEstimate(counts, conditions, params, verbose, BPPARAM)
 }
 
diff --git a/R/simple-estimate.R b/R/simple-estimate.R
index 4f09ed4b2ae5b72cd4adf68e65300b58d53d4922..3a50a4143ad591c6f0ee1790cfedd2f5903b6f3e 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 <- SummarizedExperiment::assays(counts)$counts
+    counts <- BiocGenerics::counts(counts)
     simpleEstimate(counts, params)
 }
 
diff --git a/R/splat-estimate.R b/R/splat-estimate.R
index 496edf19324b7dae80e02a5a415f43bfdd834d60..ead3c49fe500c4173e69eab9bddb2ccc48ae758f 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 <- SummarizedExperiment::assays(counts)$counts
+    counts <- BiocGenerics::counts(counts)
     splatEstimate(counts, params)
 }