Regress out total_count rather than cytoplasmArea

edsgard · May 22, 2017 · 82cc6dd · 82cc6dd
1 parent c3ae3e5
commit 82cc6dd
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Showing 8 changed files with 1,418 additions and 855 deletions.
diff --git a/Analysis/BreastCancer/Breast Cancer Tissue Analysis.ipynb b/Analysis/BreastCancer/Breast Cancer Tissue Analysis.ipynb
@@ -555,12 +555,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": []
+   "execution_count": 62,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "SE     93\n",
+       "PER    22\n",
+       "Name: model, dtype: int64"
+      ]
+     },
+     "execution_count": 62,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ms_results.model.value_counts()"
+   ]
   },
   {
    "cell_type": "code",
@@ -596,7 +609,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": []
   },

diff --git a/Analysis/Frog/Frog Development Analysis.ipynb b/Analysis/Frog/Frog Development Analysis.ipynb
diff --git a/Analysis/MERFISH/MERFISH Analysis.ipynb b/Analysis/MERFISH/MERFISH Analysis.ipynb
diff --git a/Analysis/MERFISH/Make MERFISH Expression table.ipynb b/Analysis/MERFISH/Make MERFISH Expression table.ipynb
diff --git a/Analysis/MERFISH/middle_MS_results.csv b/Analysis/MERFISH/middle_MS_results.csv
diff --git a/Analysis/MERFISH/middle_final_results.csv b/Analysis/MERFISH/middle_final_results.csv
diff --git a/Analysis/MERFISH/spatial_MERFISH_analysis.py b/Analysis/MERFISH/spatial_MERFISH_analysis.py
@@ -17,7 +17,7 @@ def main():
 
     # Convert data to log-scale, and account for depth
     dfm = NaiveDE.stabilize(df.T).T
-    res = NaiveDE.regress_out(sample_info, dfm.T, 'np.log(cytoplasmArea)').T
+    res = NaiveDE.regress_out(sample_info, dfm.T, 'np.log(total_count)').T
 
     # Perform Spatial DE test with default settings
     results = SpatialDE.run(X, res)

diff --git a/Analysis/MouseOB/Mouse Olfactory Bulb Analysis.ipynb b/Analysis/MouseOB/Mouse Olfactory Bulb Analysis.ipynb