BUG fix slogdet bug

pydeseq2/dds.py

@@ -38,7 +38,6 @@
 # Ignore AnnData's FutureWarning about implicit data conversion.
 warnings.simplefilter("ignore", FutureWarning)
 
-
 # TODO: implement a quiet (non-verbose) mode ?
 
 
@@ -764,32 +763,32 @@ def _replace_outliers(self) -> None:
         idx = self.layers["cooks"] > cooks_cutoff
         self.varm["replaced"] = idx.any(axis=0)
 
-        # Compute replacement counts: trimmed means * size_factors
-        self.counts_to_refit = self[:, self.varm["replaced"]].copy()
-
-        trim_base_mean = pd.DataFrame(
-            cast(
-                np.ndarray,
-                trimmed_mean(
-                    self.counts_to_refit.X / self.obsm["size_factors"][:, None],
-                    trim=0.2,
-                    axis=0,
+        if sum(self.varm["replaced"] > 0):
+            # Compute replacement counts: trimmed means * size_factors
+            self.counts_to_refit = self[:, self.varm["replaced"]].copy()
+
+            trim_base_mean = pd.DataFrame(
+                cast(
+                    np.ndarray,
+                    trimmed_mean(
+                        self.counts_to_refit.X / self.obsm["size_factors"][:, None],
+                        trim=0.2,
+                        axis=0,
+                    ),
                 ),
-            ),
-            index=self.counts_to_refit.var_names,
-        )
-
-        replacement_counts = (
-            pd.DataFrame(
-                trim_base_mean.values * self.obsm["size_factors"],
                 index=self.counts_to_refit.var_names,
-                columns=self.counts_to_refit.obs_names,
             )
-            .astype(int)
-            .T
-        )
 
-        if sum(self.varm["replaced"] > 0):
+            replacement_counts = (
+                pd.DataFrame(
+                    trim_base_mean.values * self.obsm["size_factors"],
+                    index=self.counts_to_refit.var_names,
+                    columns=self.counts_to_refit.obs_names,
+                )
+                .astype(int)
+                .T
+            )
+
             self.counts_to_refit.X[
                 self.obsm["replaceable"][:, None] & idx[:, self.varm["replaced"]]
             ] = replacement_counts.values[
@@ -804,15 +803,17 @@ def _refit_without_outliers(
             self.refit_cooks
         ), "Trying to refit Cooks outliers but the 'refit_cooks' flag is set to False"
 
-        # Check that replaced counts are available. If not, compute them.
-        if not hasattr(self, "counts_to_refit"):
+        # Check that _replace_outliers() was previously run.
+        if "replaced" not in self.varm:
             self._replace_outliers()
 
         # Only refit genes for which replacing outliers hasn't resulted in all zeroes
         new_all_zeroes = (self.counts_to_refit.X == 0).all(axis=0)
         self.new_all_zeroes_genes = self.counts_to_refit.var_names[new_all_zeroes]
-        self.counts_to_refit = self.counts_to_refit[:, ~new_all_zeroes].copy()
+        if (~new_all_zeroes).sum() == 0:  # if no gene can be refit, we can skip
+            return
 
+        self.counts_to_refit = self.counts_to_refit[:, ~new_all_zeroes].copy()
         if isinstance(self.new_all_zeroes_genes, pd.MultiIndex):
             raise ValueError
 
@@ -875,10 +876,13 @@ def _refit_without_outliers(
 
         self.layers["replace_cooks"] = replace_cooks
         # Take into account new all-zero genes
-        self[:, self.new_all_zeroes_genes].varm["_normed_means"] = np.zeros(
-            new_all_zeroes.sum()
-        )
-        self[:, self.new_all_zeroes_genes].varm["LFC"] = np.zeros(new_all_zeroes.sum())
+        if (new_all_zeroes).sum() > 0:
+            self[:, self.new_all_zeroes_genes].varm["_normed_means"] = np.zeros(
+                new_all_zeroes.sum()
+            )
+            self[:, self.new_all_zeroes_genes].varm["LFC"] = np.zeros(
+                new_all_zeroes.sum()
+            )
 
     def _fit_iterate_size_factors(self, niter: int = 10, quant: float = 0.95) -> None:
         """

pydeseq2/utils.py

@@ -233,7 +233,7 @@ def build_design_matrix(
 
     if intercept:
         design_matrix.insert(0, "intercept", 1)
-    return design_matrix
+    return design_matrix.astype("int")
 
 
 def dispersion_trend(