diff --git a/examples/GSE108041/Seurat_v3/README.md b/examples/GSE108041/Seurat_v3/README.md
index c3c05824..0883d4c6 100755
--- a/examples/GSE108041/Seurat_v3/README.md
+++ b/examples/GSE108041/Seurat_v3/README.md
@@ -277,8 +277,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@assays$RNA@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
@@ -302,8 +302,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@assays$RNA@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
diff --git a/examples/GSE108041/scanpy/README.md b/examples/GSE108041/scanpy/README.md
index 93877202..56a12bc8 100755
--- a/examples/GSE108041/scanpy/README.md
+++ b/examples/GSE108041/scanpy/README.md
@@ -353,8 +353,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@assays$RNA@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
@@ -378,8 +378,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@assays$RNA@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
diff --git a/examples/GSE129845/Seurat_v3/README.md b/examples/GSE129845/Seurat_v3/README.md
index 29572205..d1cf7375 100644
--- a/examples/GSE129845/Seurat_v3/README.md
+++ b/examples/GSE129845/Seurat_v3/README.md
@@ -341,8 +341,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@assays$RNA@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
@@ -366,8 +366,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@assays$RNA@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
diff --git a/examples/pbmc_10k_v3/Seurat_v2/README.md b/examples/pbmc_10k_v3/Seurat_v2/README.md
index ea6ee28b..b6af60a7 100755
--- a/examples/pbmc_10k_v3/Seurat_v2/README.md
+++ b/examples/pbmc_10k_v3/Seurat_v2/README.md
@@ -286,8 +286,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@data),
-    row.names = rownames(seurat@data))
+    gene_short_name = rownames(seurat@counts),
+    row.names = rownames(seurat@counts))
   )
 )
 
@@ -311,8 +311,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@data),
-    row.names = rownames(seurat@data))
+    gene_short_name = rownames(seurat@counts),
+    row.names = rownames(seurat@counts))
   )
 )
 
diff --git a/examples/pbmc_10k_v3/Seurat_v3/README.md b/examples/pbmc_10k_v3/Seurat_v3/README.md
index 8a4162e5..1b2d428a 100755
--- a/examples/pbmc_10k_v3/Seurat_v3/README.md
+++ b/examples/pbmc_10k_v3/Seurat_v3/README.md
@@ -233,8 +233,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@assays$RNA@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
@@ -258,8 +258,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@assays$RNA@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
diff --git a/examples/pbmc_10k_v3/scanpy/README.md b/examples/pbmc_10k_v3/scanpy/README.md
index 42b8e237..4165700d 100755
--- a/examples/pbmc_10k_v3/scanpy/README.md
+++ b/examples/pbmc_10k_v3/scanpy/README.md
@@ -321,8 +321,8 @@ monocle_all_cells <- newCellDataSet(
   seurat@assays$RNA@data,
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )
 
@@ -346,8 +346,8 @@ monocle_subset_of_cells <- newCellDataSet(
   seurat@assays$RNA@data[,G1_cells],
   phenoData = new('AnnotatedDataFrame', data = seurat@meta.data[G1_cells,]),
   featureData = new('AnnotatedDataFrame', data = data.frame(
-    gene_short_name = rownames(seurat@assays$RNA@data),
-    row.names = rownames(seurat@assays$RNA@data))
+    gene_short_name = rownames(seurat@assays$RNA@counts),
+    row.names = rownames(seurat@assays$RNA@counts))
   )
 )