--- a
+++ b/tests/deseq2/test_methods.py
@@ -0,0 +1,39 @@
+import unittest
+
+import numpy as np
+import pandas as pd
+
+from inmoose.deseq2 import DESeqDataSet
+from inmoose.utils import Factor
+
+
+class Test(unittest.TestCase):
+    def test_method_errors(self):
+        """test that methods throw errors"""
+        coldata = pd.DataFrame({"x": Factor(["A", "A", "B", "B"])})
+        counts = np.arange(1, 17).reshape((4, 4))
+        dds = DESeqDataSet(counts, coldata, "~x")
+        with self.assertLogs("inmoose", level="WARNING") as logChecker:
+            dds.counts(replaced=True)
+        self.assertRegex(
+            logChecker.output[0],
+            "There is no layer named 'replacedCounts', using original.",
+        )
+        with self.assertRaisesRegex(
+            ValueError,
+            expected_regex="first calculate size factors, add normalizationFactors, or set normalized=False",
+        ):
+            dds.counts(normalized=True)
+        with self.assertRaisesRegex(
+            ValueError, expected_regex="size factors should be positive"
+        ):
+            dds.sizeFactors = [-1, -1, -1, -1]
+        with self.assertRaisesRegex(
+            ValueError, expected_regex="normalization factors should be positive"
+        ):
+            dds.normalizationFactors = np.full((4, 4), -1)
+        with self.assertRaisesRegex(
+            ValueError,
+            expected_regex="first call estimateSizeFactors or provide a normalizationFactor matrix before calling estimateDispersions",
+        ):
+            dds.estimateDispersions()