diff --git a/R/MsExperiment.R b/R/MsExperiment.R
index 9ecba6c..2ffff28 100644
--- a/R/MsExperiment.R
+++ b/R/MsExperiment.R
@@ -300,16 +300,16 @@ setMethod("readMsObject",
 .clean_merged <- function(x, keepProtocol, keepOntology, simplify) {
     # remove ontology
     if (!keepOntology)
-        x <- x[, -which(grepl("Term", names(x)))]
+        x <- x[, -which(grepl("Term", names(x))), drop = FALSE]
 
     # remove protocol
     if (!keepProtocol)
-        x <- x[, -which(grepl("Protocol|Parameter", names(x)))]
+        x <- x[, -which(grepl("Protocol|Parameter", names(x))),  drop = FALSE]
 
     # remove duplicated columns contents and NAs
     if (simplify) {
-        x <- x[, !duplicated(as.list(x))]
-        x <- x[, colSums(is.na(x)) != nrow(x)]
+        x <- x[, !duplicated(as.list(x)), drop = FALSE]
+        x <- x[, colSums(is.na(x)) != nrow(x), drop = FALSE]
     }
     return(x)
 }
diff --git a/tests/testthat/test_MetaboLightsParam.R b/tests/testthat/test_MetaboLightsParam.R
index d42b378..fcc16c0 100644
--- a/tests/testthat/test_MetaboLightsParam.R
+++ b/tests/testthat/test_MetaboLightsParam.R
@@ -33,3 +33,42 @@ test_that("interactive session works", {
     expect_true(ncol(result@sampleData) == 30)
 })
 
+test_that(".clean_merged function works correctly", {
+    tbc <- data.frame(
+        Protocol_A = c(1, 2, 3),
+        Term_B = c("ontology1", "ontology2", "ontology3"),
+        Parameter_C = c(10, 20, 30),
+        Term_D = c("ontology1", "ontology2", "ontology3"),
+        Data_E = c(NA, NA, NA),
+        Duplicate_F = c(1, 2, 3),
+        stringsAsFactors = FALSE
+    )
+    result <- .clean_merged(tbc, keepProtocol = TRUE,
+                            keepOntology = TRUE,
+                            simplify = FALSE)
+    expect_equal(names(result), names(tbc))
+
+    result <- .clean_merged(tbc, keepProtocol = TRUE,
+                            keepOntology = FALSE, simplify = FALSE)
+    expect_equal(names(result), c("Protocol_A", "Parameter_C", "Data_E",
+                                  "Duplicate_F"))
+
+    result <- .clean_merged(tbc, keepProtocol = FALSE,
+                            keepOntology = TRUE, simplify = FALSE)
+    expect_equal(names(result), c("Term_B", "Term_D", "Data_E", "Duplicate_F"))
+
+    result <- .clean_merged(tbc, keepProtocol = FALSE, keepOntology = FALSE,
+                            simplify = FALSE)
+    expect_equal(names(result), c("Data_E", "Duplicate_F"))
+
+    result <- .clean_merged(tbc, keepProtocol = TRUE, keepOntology = TRUE,
+                            simplify = TRUE)
+    expect_equal(names(result), c("Protocol_A", "Term_B", "Parameter_C"))
+
+
+    result <- .clean_merged(tbc, keepProtocol = FALSE, keepOntology = FALSE,
+                            simplify = TRUE)
+    expect_equal(names(result), "Duplicate_F")
+})
+
+