diff --git a/app/Main.hs b/app/Main.hs
--- a/app/Main.hs
+++ b/app/Main.hs
@@ -101,7 +101,7 @@
                , minModularity :: Maybe Double <?> "([Nothing] | DOUBLE) Nearly the same as --min-distance, but for clustering instead of drawing (so the output json tree can be larger). Stopping criteria to stop at the node with DOUBLE modularity. So a node N with L and R children will stop with this criteria the distance at N to L and R is < DOUBLE. Does not include L and R in the final result."
                , minDistance :: Maybe Double <?> "([Nothing] | DOUBLE) Stopping criteria to stop at the node immediate after a node with DOUBLE distance. So a node N with L and R children will stop with this criteria the distance at N to L and R is < DOUBLE. Includes L and R in the final result."
                , minDistanceSearch :: Maybe Double <?> "([Nothing] | DOUBLE) Similar to --min-distance, but searches from the leaves to the root -- if a path from a subtree contains a distance of at least DOUBLE, keep that path, otherwise prune it. This argument assists in finding distant nodes."
-               , smartCutoff :: Maybe Double <?> "([Nothing] | DOUBLE) Whether to set the cutoffs for --min-size, --max-proportion, --min-distance, and --min-distance-search based off of the distributions (median + (DOUBLE * MAD)) of all nodes. To use smart cutoffs, use this argument and then set one of the three arguments to an arbitrary number, whichever cutoff type you want to use. --min-size distribution is log2 transformed."
+               , smartCutoff :: Maybe Double <?> "([Nothing] | DOUBLE) Whether to set the cutoffs for --min-size, --max-proportion, --min-distance, and --min-distance-search based off of the distributions (median + (DOUBLE * MAD)) of all nodes. To use smart cutoffs, use this argument and then set one of the four arguments to an arbitrary number, whichever cutoff type you want to use. --min-proportion distribution is log2 transformed."
                , customCut :: [Int] <?> "([Nothing] | NODE) List of nodes to prune (make these nodes leaves). Invoked by --custom-cut 34 --custom-cut 65 etc."
                , dendrogramOutput :: Maybe String <?> "([dendrogram.svg] | FILE) The filename for the dendrogram. Supported formats are PNG, PS, PDF, and SVG."
                , matrixOutput :: Maybe String <?> "([Nothing] | FOLDER | FILE.csv) Output the filtered and normalized (not including TfIdfNorm) matrix in this folder under the --output directory in matrix market format or, if a csv file is specified, a dense csv format. Like input, features are rows. See --matrix-output-transpose."
@@ -347,6 +347,8 @@
 
     -- Check for empty matrix.
     when (V.null . getRowNames $ processedSc) $ error "Matrix is empty. Check --filter-thresholds, --normalization, or the input matrix for over filtering or incorrect input format."
+
+    liftIO . mapM_ print . matrixValidity $ processedSc
 
     return processedSc
 
diff --git a/src/TooManyCells/Matrix/Utility.hs b/src/TooManyCells/Matrix/Utility.hs
--- a/src/TooManyCells/Matrix/Utility.hs
+++ b/src/TooManyCells/Matrix/Utility.hs
@@ -22,6 +22,7 @@
     , writeMatrixLike
     , isCsvFile
     , getMatrixOutputType
+    , matrixValidity
     ) where
 
 -- Remote
@@ -234,3 +235,22 @@
 -- | Get matrix output format from input name.
 getMatrixOutputType :: FilePath -> MatrixFileFolder
 getMatrixOutputType x = bool (MatrixFolder x) (MatrixFile x) . isCsvFile $ x
+
+-- | Check validity of matrix.
+matrixValidity :: (MatrixLike a) => a -> Maybe String
+matrixValidity mat
+  | rows /= numCells || cols /= numFeatures =
+      Just $ "Warning: mismatch in number of (features, cells) ("
+                           <> show numFeatures
+                           <> ","
+                           <> show numCells
+                           <> ") with matrix (rows, columns) ("
+                           <> show cols
+                           <> ","
+                           <> show rows
+                           <> "), will probably result in error."
+  | otherwise = Nothing
+  where
+    (rows, cols) = S.dimSM . getMatrix $ mat
+    numCells = V.length . getRowNames $ mat
+    numFeatures = V.length . getColNames $ mat
diff --git a/too-many-cells.cabal b/too-many-cells.cabal
--- a/too-many-cells.cabal
+++ b/too-many-cells.cabal
@@ -1,6 +1,6 @@
 cabal-version: >=1.10
 name: too-many-cells
-version: 0.1.12.1
+version: 0.1.12.2
 license: GPL-3
 license-file: LICENSE
 copyright: 2019 Gregory W. Schwartz
@@ -65,7 +65,7 @@
         foldl >=1.4.2,
         graphviz >=2999.20.0.2,
         hierarchical-clustering >=0.4.6,
-        hierarchical-spectral-clustering >=0.4.0.2,
+        hierarchical-spectral-clustering >=0.4.1.1,
         hmatrix >=0.19.0.0,
         inline-r >=0.9.2,
         lens >=4.16.1,
@@ -114,7 +114,7 @@
         filepath >=1.4.2,
         find-clumpiness >=0.2.3.1,
         graphviz >=2999.20.0.2,
-        hierarchical-spectral-clustering >=0.4.0.2,
+        hierarchical-spectral-clustering >=0.4.1.1,
         inline-r >=0.9.2,
         lens >=4.16.1,
         matrix-market-attoparsec >=0.1.0.8,