diff --git a/R/merge_sce_list.R b/R/merge_sce_list.R
index 6a2b8ec9..5a0f3954 100644
--- a/R/merge_sce_list.R
+++ b/R/merge_sce_list.R
@@ -61,8 +61,6 @@ merge_sce_list <- function(
     preserve_rowdata_cols = NULL,
     cell_id_column = "cell_id",
     include_altexp = TRUE) {
-
-  ## Checks --------------------------
   if (is.null(names(sce_list))) {
     warning(
       glue::glue(
@@ -70,7 +68,7 @@ merge_sce_list <- function(
         named based on their list index in the merged SCE object."
       )
     )
-    names(sce_list) <- 1:length(sce_list)
+    names(sce_list) <- seq_along(sce_list)
   }
 
   if (length(sce_list) < 2) {
@@ -96,13 +94,14 @@ merge_sce_list <- function(
     coldata_suffixes <- c("sum", "detected", "percent")
     altexp_columns <- glue::glue("altexps_{names(altexp_attributes)}") |>
       purrr::map(
-        \(prefix) { glue::glue("{prefix}_{coldata_suffixes}")}
+        \(prefix) {
+          glue::glue("{prefix}_{coldata_suffixes}")
+        }
       ) |>
       unlist()
 
     # Update retain_coldata_cols
     retain_coldata_cols <- c(retain_coldata_cols, altexp_columns)
-
   } else {
     # Remove altexps if we are not including them
     sce_list <- sce_list |>
@@ -139,7 +138,7 @@ merge_sce_list <- function(
 
   # check that library id and sample id are present in metadata
   id_checks <- sce_list |>
-    purrr::map(\(sce){
+    purrr::map(\(sce) {
       all(c("library_id", "sample_id") %in% names(metadata(sce)))
     }) |>
     unlist()
@@ -196,9 +195,7 @@ merge_sce_list <- function(
 
   # If we are including altExps, process them and save to list to add to merged SCE
   if (include_altexp) {
-
     for (altexp_name in names(altexp_attributes)) {
-
       expected_assays <- altexp_attributes[[altexp_name]][["assays"]]
       expected_features <- altexp_attributes[[altexp_name]][["features"]]
 
@@ -215,7 +212,7 @@ merge_sce_list <- function(
   }
 
   # Create the merged SCE from the processed list
-  merged_sce <- do.call(cbind, sce_list)
+  merged_sce <- do.call(combineCols, unname(sce_list))
 
   # Replace existing metadata list with merged metadata
   metadata(merged_sce) <- metadata_list
@@ -245,15 +242,14 @@ merge_sce_list <- function(
 #'
 #' @return An updated SCE that is prepared for merging
 prepare_sce_for_merge <- function(
-  sce,
-  sce_name,
-  batch_column,
-  cell_id_column,
-  shared_features,
-  retain_coldata_cols,
-  preserve_rowdata_cols,
-  is_altexp = FALSE) {
-
+    sce,
+    sce_name,
+    batch_column,
+    cell_id_column,
+    shared_features,
+    retain_coldata_cols,
+    preserve_rowdata_cols,
+    is_altexp = FALSE) {
   # Subset to shared features
   sce <- sce[shared_features, ]
 
@@ -337,18 +333,8 @@ prepare_altexp_for_merge <- function(
     batch_column,
     cell_id_column,
     preserve_rowdata_cols = c("target_type")) {
-
-  if (!altexp_name %in% altExpNames(sce) ) {
-
-    na_assays <- expected_assays |>
-      purrr::set_names() |>
-      purrr::map(
-        build_na_matrix,
-        expected_features,
-        colnames(sce)
-      )
-
-    altExp(sce, altexp_name) <- SingleCellExperiment(assays = na_assays)
+  if (!altexp_name %in% altExpNames(sce)) {
+    return(sce)
   }
 
   # Now, prepare this altexp for merge
@@ -374,10 +360,12 @@ prepare_altexp_for_merge <- function(
 #'
 #' @return Updated metadata list to store in the SCE
 update_sce_metadata <- function(metadata_list) {
-
   # first check that this library hasn't already been merged
   if ("library_metadata" %in% names(metadata_list)) {
-    stop("This SCE object appears to be a merged object. We do not support merging objects with objects that have already been merged.")
+    stop(paste(
+      "This SCE object appears to be a merged object",
+      "We do not support merging objects with objects that have already been merged."
+    ))
   }
 
   # create library and sample metadata.
@@ -398,33 +386,6 @@ update_sce_metadata <- function(metadata_list) {
 }
 
 
-
-
-#' Create a sparse matrix with all NA values
-#'
-#' @param assay_name Intended assay name for this matrix (e.g., "counts")
-#' @param matrix_rownames Vector of matrix rown ames
-#' @param matrix_colnames Vector of matrix column names
-#'
-#' @return Sparse matrix
-build_na_matrix <- function(
-    assay_name,
-    matrix_rownames,
-    matrix_colnames) {
-
-  Matrix::Matrix(
-    data = NA_real_,
-    nrow = length(matrix_rownames),
-    ncol = length(matrix_colnames),
-    dimnames = list(
-      matrix_rownames,
-      matrix_colnames
-    ),
-    sparse = TRUE
-  )
-}
-
-
 #' Helper function to check altExp compatibility
 #'
 #' @param sce_list List of SCEs with altExps to check
@@ -433,7 +394,6 @@ build_na_matrix <- function(
 #'   with each sublist formatted as:
 #'   altexp_name = list(features = c(features), assays = c(assays))
 get_altexp_attributes <- function(sce_list) {
-
   # Attribute list to save for later use
   altexp_attributes <- list()
 
@@ -445,7 +405,6 @@ get_altexp_attributes <- function(sce_list) {
   # For each in altexp_names (if present), do they have the same features?
   # If not, error out
   for (altexp_name in altexp_names) {
-
     # all altExps for this name
     altexp_list <- sce_list |>
       purrr::keep(\(sce) altexp_name %in% altExpNames(sce)) |>
@@ -473,25 +432,11 @@ get_altexp_attributes <- function(sce_list) {
       purrr::map(assayNames) |>
       purrr::reduce(union)
 
-    # create logical vector for presence of all assays
-    assays_present <- altexp_list |>
-      purrr::map_lgl(
-        \(alt_sce) setequal(assayNames(alt_sce), all_assays)
-      )
-
-    # TODO: we may want to drop assays that aren't present in all altexps, rather than dying.
-    if (!all(assays_present)) {
-      stop(
-        glue::glue("The {altexp_name} alternative experiments do not share the same set of assays.")
-      )
-    }
-
     # Save to altexp_attributes for later use
     altexp_attributes[[altexp_name]] <- list(
       "features" = all_features,
       "assays"   = all_assays
     )
-
   }
   return(altexp_attributes)
 }
diff --git a/man/build_na_matrix.Rd b/man/build_na_matrix.Rd
deleted file mode 100644
index 45fc6b9b..00000000
--- a/man/build_na_matrix.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/merge_sce_list.R
-\name{build_na_matrix}
-\alias{build_na_matrix}
-\title{Create a sparse matrix with all NA values}
-\usage{
-build_na_matrix(assay_name, matrix_rownames, matrix_colnames)
-}
-\arguments{
-\item{assay_name}{Intended assay name for this matrix (e.g., "counts")}
-
-\item{matrix_rownames}{Vector of matrix rown ames}
-
-\item{matrix_colnames}{Vector of matrix column names}
-}
-\value{
-Sparse matrix
-}
-\description{
-Create a sparse matrix with all NA values
-}
diff --git a/tests/testthat/test-merge_sce_list.R b/tests/testthat/test-merge_sce_list.R
index 069c2eb6..e546eb89 100644
--- a/tests/testthat/test-merge_sce_list.R
+++ b/tests/testthat/test-merge_sce_list.R
@@ -60,7 +60,6 @@ sce_list <- list(
 # Tests without altexps ----------------------------------------------
 
 test_that("`update_sce_metadata()` returns the expected list", {
-
   metadata_list <- metadata(sce_list[[1]])
 
   new_metadata <- update_sce_metadata(metadata_list)
@@ -72,7 +71,7 @@ test_that("`update_sce_metadata()` returns the expected list", {
 
   expect_equal(
     names(new_metadata$library_metadata),
-    c("library_id",  "sample_id", "total_reads")
+    c("library_id", "sample_id", "total_reads")
   )
 })
 
@@ -327,7 +326,7 @@ test_that("merging SCEs with library metadata fails as expected, no altexps", {
   expect_error(
     merge_sce_list(
       sce_list
-      )
+    )
   )
 })
 
@@ -341,15 +340,22 @@ add_sce_altexp <- function(
     altexp_name,
     num_altexp_features,
     n_cells) {
-
   sce_alt <- sim_sce(
     n_genes = num_altexp_features,
     n_cells = n_cells,
-    n_empty = 0)
+    n_empty = 0
+  )
 
   # ensure matching barcodes
   colnames(sce_alt) <- colnames(sce)
 
+  # change feature names
+  rownames(sce_alt) <- stringr::str_replace(
+    rownames(sce_alt),
+    "^GENE",
+    toupper(altexp_name)
+  )
+
   # add some rowdata columns
   rowData(sce_alt)[["target_type"]] <- "target" # should be retained
   rowData(sce_alt)[["feature_column"]] <- rownames(sce_alt)
@@ -395,7 +401,6 @@ full_altexp_features <- rownames(altExp(sce_list_with_altexp[[1]]))
 
 
 test_that("prepare_sce_for_merge() works as expected with is_altexp=TRUE", {
-
   test_altexp <- altExp(sce_list_with_altexp[[1]])
   prepared_altexp <- prepare_sce_for_merge(
     test_altexp,
@@ -424,51 +429,7 @@ test_that("prepare_sce_for_merge() works as expected with is_altexp=TRUE", {
 })
 
 
-test_that("prepare_sce_for_merge() works from an NA matrix", {
-
-
-  assay_names <- c("counts", "logcounts")
-  sce <- sce_list_with_altexp[[1]]
-  na_assays <- assay_names |>
-    purrr::set_names() |>
-    purrr::map(
-      build_na_matrix,
-      full_altexp_features,
-      colnames(sce)
-    )
-  test_altexp <- SingleCellExperiment(assays = na_assays)
-
-  prepared_altexp <- prepare_sce_for_merge(
-    test_altexp,
-    "test",
-    batch_column = batch_column,
-    cell_id_column = cell_id_column,
-    shared_features = full_altexp_features,
-    retain_coldata_cols = NULL,
-    preserve_rowdata_cols = c("target_type"),
-    is_altexp = TRUE
-  )
-
-  expect_equal(
-    assayNames(prepared_altexp), assay_names
-  )
-
-  expect_equal(
-    colnames(colData(prepared_altexp)), c("batch", "cell_id")
-  )
-
-  expect_equal(
-    colnames(prepared_altexp), colnames(sce)
-  )
-
-  expect_equal(
-    rownames(prepared_altexp), full_altexp_features
-  )
-})
-
-
 test_that("merging SCEs with altExps works as expected when include_altexps = FALSE", {
-
   merged_sce <- merge_sce_list(
     sce_list_with_altexp,
     batch_column = batch_column,
@@ -481,11 +442,9 @@ test_that("merging SCEs with altExps works as expected when include_altexps = FA
 
   # there should not be any altExps
   expect_length(altExpNames(merged_sce), 0)
-
 })
 
 test_that("merging SCEs with 1 altexp and same features works as expected, with altexps", {
-
   merged_sce <- merge_sce_list(
     sce_list_with_altexp,
     batch_column = batch_column,
@@ -511,13 +470,15 @@ test_that("merging SCEs with 1 altexp and same features works as expected, with
   expect_equal(colnames(merged_altexp), expected_colnames)
 
   # Check colData columns
-  expected_coldata <- c("sum",
-                        "detected",
-                        "altexps_adt_sum",
-                        "altexps_adt_detected",
-                        "altexps_adt_percent",
-                        batch_column,
-                        "cell_id")
+  expected_coldata <- c(
+    "sum",
+    "detected",
+    "altexps_adt_sum",
+    "altexps_adt_detected",
+    "altexps_adt_percent",
+    batch_column,
+    "cell_id"
+  )
 
   expect_true(
     setequal(
@@ -525,16 +486,14 @@ test_that("merging SCEs with 1 altexp and same features works as expected, with
       expected_coldata
     )
   )
-
 })
 
 
 
 
 test_that("merging SCEs with 1 altexp but different features fails as expected, with altexps", {
-
   # keep only the first 3 features from the first SCE
-  altExp(sce_list_with_altexp[[1]]) <- altExp(sce_list_with_altexp[[1]])[1:3,]
+  altExp(sce_list_with_altexp[[1]]) <- altExp(sce_list_with_altexp[[1]])[1:3, ]
 
 
   expect_error(
@@ -553,12 +512,11 @@ test_that("merging SCEs with 1 altexp but different features fails as expected,
 
 
 test_that("merging SCEs where 1 altExp is missing works as expected, with altexps", {
-
   sce_list_with_altexp[["sce4"]] <- removeAltExps(sce_list_with_altexp[[1]])
 
   # from cbind docs:
-  #The colnames in colData(SummarizedExperiment) must match or an error is thrown.
-  #Duplicate columns of rowData(SummarizedExperiment) must contain the same data.
+  # The colnames in colData(SummarizedExperiment) must match or an error is thrown.
+  # Duplicate columns of rowData(SummarizedExperiment) must contain the same data.
 
   merged_sce <- merge_sce_list(
     sce_list_with_altexp,
@@ -570,37 +528,12 @@ test_that("merging SCEs where 1 altExp is missing works as expected, with altexp
   )
 
   expect_equal(altExpNames(merged_sce), "adt")
-
 })
 
 
 ## Other tests ------------------
 
-test_that("build_na_matrix works as expected",{
-
-  rows <- letters[1:5]
-  cols  <- letters[6:10]
-  sparse_mat <- build_na_matrix(
-    "name",
-    rows,
-    cols
-  )
-
-  expect_s4_class(sparse_mat, "sparseMatrix")
-
-  expect_equal(
-    rownames(sparse_mat), rows
-  )
-
-  expect_equal(
-    colnames(sparse_mat), cols
-  )
-
-})
-
-
 test_that("get_altexp_attributes passes when it should pass", {
-
   attribute_list <- get_altexp_attributes(sce_list_with_altexp)
   expect_equal(
     attribute_list[["adt"]][["assays"]], c("counts", "logcounts")
@@ -608,20 +541,10 @@ test_that("get_altexp_attributes passes when it should pass", {
   expect_equal(
     attribute_list[["adt"]][["features"]], full_altexp_features
   )
-
 })
 
 
-test_that("get_altexp_attributes throws an error as expected when assays do not match", {
-
-  logcounts(altExp(sce_list_with_altexp[[3]])) <- NULL
-  expect_error(get_altexp_attributes(sce_list_with_altexp))
-
-})
-
 test_that("get_altexp_attributes throws an error as expected when features do not match", {
-
-  altExp(sce_list_with_altexp[[1]]) <- altExp(sce_list_with_altexp[[1]])[1:3,]
+  altExp(sce_list_with_altexp[[1]]) <- altExp(sce_list_with_altexp[[1]])[1:3, ]
   expect_error(get_altexp_attributes(sce_list_with_altexp))
-
 })