diff --git a/R/makeShinyFilesDEG.R b/R/makeShinyFilesDEG.R
index 806eee4..03b2aae 100644
--- a/R/makeShinyFilesDEG.R
+++ b/R/makeShinyFilesDEG.R
@@ -121,6 +121,28 @@ makeShinyFilesDEG <- function(
     )
   }
 
+  # Validate DEG cluster levels match metadata cluster levels
+  deg_clusters <- sort(unique(as.character(markergenes$cluster)))
+  meta_clusters <- sort(unique(as.character(obj@meta.data[[clusters]])))
+  if (!all(deg_clusters %in% meta_clusters)) {
+    missing <- setdiff(deg_clusters, meta_clusters)
+    stop(
+      "DEG markers contain cluster(s) not found in metadata column '", clusters, "': ",
+      paste(missing, collapse = ", "),
+      "\n  DEG clusters: ", paste(deg_clusters, collapse = ", "),
+      "\n  Metadata clusters: ", paste(meta_clusters, collapse = ", ")
+    )
+  }
+
+  # Validate that the clusters column exists in scConf (i.e. it was not filtered out)
+  if (!clusters %in% scConf$ID && !clusters %in% scConf$UI) {
+    stop(
+      "Cluster label '", clusters, "' was not included in the ShinyCell config (sc1conf). ",
+      "It may have been removed by metadata filtering (rmmeta/unsupported assay pattern). ",
+      "Please ensure this column is retained in the config."
+    )
+  }
+
   # markergene h5 creation
   n_rows <- nrow(markergenes)
   n_cols <- ncol(markergenes)
diff --git a/R/writer1.R b/R/writer1.R
index eb32a8d..ea86d3d 100644
--- a/R/writer1.R
+++ b/R/writer1.R
@@ -131,8 +131,8 @@ wrSVmainA1 <- function(prefix) {
     '    return(list(res,resDef,resLen))\n',
     '  }})\n',
     '  observeEvent(gsub("^Assay: ", "", input${prefix}a1ass1), {{\n',
-    '    updateSelectizeInput(session, "{prefix}a1inp1", choices = getG{prefix}a1inp1()[[1]], \n',
-    '                         server = TRUE, selected = getG{prefix}a1inp1()[[2]], options = list( \n',
+  '    updateSelectizeInput(session, "{prefix}a1inp1", choices = getG{prefix}a1inp1()[[1]], \n',
+  '                         server = TRUE, selected = getG{prefix}a1inp1()[[1]][1], options = list( \n',
     '                           maxOptions = getG{prefix}a1inp1()[[3]], create = TRUE, \n',
     '                           persist = TRUE, render = I(optCrt))) \n',
     '  }})\n',
diff --git a/R/writer2.R b/R/writer2.R
index d721744..178d87d 100644
--- a/R/writer2.R
+++ b/R/writer2.R
@@ -149,7 +149,9 @@ wrUImainA1 <- function(prefix, ptsiz) {
     '        selectInput("{prefix}a1ass1", "Data type to colour plot:",\n',
     '                    choices = c("Cell Information", paste0("Assay: ", {prefix}def$assay)), \n',
     '                    selected = "Cell Information"), \n',
-    '        selectInput("{prefix}a1inp1", "Cell Info / Feature Name:", choices = NULL) %>% \n',
+  '        selectInput("{prefix}a1inp1", "Cell Info / Feature Name:", \n',
+  '                    choices = {prefix}conf$UI, \n',
+  '                    selected = {prefix}conf$UI[1]) %>% \n',
     '          helper(type = "inline", size = "m", fade = TRUE,\n',
     '                 title = "Cell Info / Gene to colour cells by",\n',
     '                 content = c("Select cell info / feature to colour cells",\n',