--- a
+++ b/tests/deseq2/test_DESeqDataSet.py
@@ -0,0 +1,53 @@
+import unittest
+
+import numpy as np
+from pandas.api.types import CategoricalDtype
+
+from inmoose.deseq2 import DESeqDataSet
+
+
+class Test(unittest.TestCase):
+    def test_counts(self):
+        """test that normalized counts are properly computed"""
+        dds = DESeqDataSet(
+            np.arange(24).reshape(4, 6), clinicalData=["A", "A", "B", "B"], design="~1"
+        )
+        with self.assertRaisesRegex(
+            ValueError,
+            expected_regex="first calculate size factors, add normalizationFactors, or set normalized=False",
+        ):
+            dds.counts(normalized=True)
+        dds = dds.estimateSizeFactors()
+        ref = np.array(
+            [
+                [0.000000, 3.201086, 6.402172, 9.603258, 12.80434, 16.00543],
+                [6.402172, 7.469200, 8.536229, 9.603258, 10.67029, 11.73731],
+                [7.682606, 8.322823, 8.963040, 9.603258, 10.24347, 10.88369],
+                [8.231364, 8.688662, 9.145960, 9.603258, 10.06056, 10.51785],
+            ]
+        )
+        res = dds.counts(normalized=True)
+        self.assertTrue(np.allclose(res, ref))
+
+    def test_design(self):
+        """test that categorical variable in the design are properly accounted for"""
+        dds = DESeqDataSet(np.arange(24).reshape(4, 6))
+        dds.obs["x"] = ["A", "A", "B", "B"]
+        dds.obs["y"] = [1, 2, 1, 2]
+        dds.design = "x + y"
+        self.assertTrue("C(x)" in dds.obs)
+        self.assertTrue("C(y)" not in dds.obs)
+        self.assertFalse(isinstance(dds.obs["x"].dtype, CategoricalDtype))
+        self.assertTrue(isinstance(dds.obs["C(x)"].dtype, CategoricalDtype))
+        self.assertFalse(isinstance(dds.obs["y"].dtype, CategoricalDtype))
+
+        dds = DESeqDataSet(np.arange(24).reshape(4, 6))
+        dds.obs["x"] = ["A", "A", "B", "B"]
+        dds.obs["y"] = [1, 2, 1, 2]
+        dds.design = "C(x) + C(y)"
+        self.assertTrue("C(x)" in dds.obs)
+        self.assertTrue("C(y)" in dds.obs)
+        self.assertFalse(isinstance(dds.obs["x"].dtype, CategoricalDtype))
+        self.assertTrue(isinstance(dds.obs["C(x)"].dtype, CategoricalDtype))
+        self.assertFalse(isinstance(dds.obs["y"].dtype, CategoricalDtype))
+        self.assertTrue(isinstance(dds.obs["C(y)"].dtype, CategoricalDtype))