Changeset 1060

Timestamp:

May 11, 2009, 1:06:16 PM (14 years ago)

Author:

Martin Svensson

Message:

Fixes #195 Normalizers should ask user for how to calculate averages

File:

• plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/AverageNormalization.java (modified) (7 diffs)

plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/AverageNormalization.java

@@ -32 +32 @@
 import net.sf.basedb.core.DynamicSpotQuery;
 import net.sf.basedb.core.FloatParameterType;
+import net.sf.basedb.core.IntensityTransform;
 import net.sf.basedb.core.InvalidUseOfNullException;
 import net.sf.basedb.core.Job;
@@ -89 +90 @@
   private static final String yesOption = "yes";
   private static final String noOption = "no";
+  private static final String geometricOption = "geometric";
+  private static final String arithmeticOption = "arithmetic";
   
   /*
@@ -123 +126 @@
     "This parameter cannot be null if 'Use global geometric mean intensity' is " + noOption + ".",
     new FloatParameterType(null, null, 100f, false)
+  );
+  
+  /*
+    Define which average method to use when calculating.
+   */
+  private PluginParameter<String> averageMethodParameter = new PluginParameter<String>
+  (
+    "averageMethod",
+    "Average calculation method",
+    "Select which method to use when calculating the averages.\n" +
+    "Geometric mean is default for none-logged values and arithmetic " +
+    "is default for logged values.",
+    null
   );
     
@@ -212 +228 @@
         storeValue(job, request, ri.getParameter(CHILD_DESCRIPTION)); 
         // Average specific parameters
+        storeValue(job, request, averageMethodParameter);
         storeValue(job, request, minIntensityParameter);
         storeValue(job, request, ri.getParameter("useGlobalAvgInt"));
-        
+                
         // Reference value cannot be null if the global average intensity shouldn't be used.
         String useGlobal = (String)request.getParameterValue("useGlobalAvgInt");
@@ -374 +391 @@
 
         // Average normalization options
+        StringParameterType spt = new StringParameterType
+        (
+            null, 
+            bas.getIntensityTransform().equals(IntensityTransform.NONE) ? geometricOption : arithmeticOption , 
+            true, 1, 0, 0, 
+            Arrays.asList(new String[] {geometricOption, arithmeticOption} )
+        );
+        averageMethodParameter = new PluginParameter<String>
+        (
+          averageMethodParameter.getName(),
+          averageMethodParameter.getLabel(),
+          averageMethodParameter.getDescription(),
+          spt
+        );
         parameters.add(normalizationSection);
+        parameters.add(averageMethodParameter);
         parameters.add(minIntensityParameter);
         parameters.add(useGlobalAverageIntensityParameter);
@@ -405 +437 @@
     long numSpots;
     long normalizedSpots = 0;
+    
+    boolean useGeometricMean = geometricOption.equals(job.getParameterValue("averageMethod"));
     
     // Create Transformation
@@ -483 +517 @@
         // Calculate the average intensity for the current assay.
         double sum = 0;
-        for (Normalizable d : data)
-        {
-          sum = sum + Math.log(d.getNormalizableData());
-        }
-        float assayAverage = (float)Math.exp(sum/dataSize);
+        float assayAverage;
+        if (useGeometricMean)
+        {
+          for (Normalizable d : data)
+          {
+            sum = sum + Math.log(d.getNormalizableData());
+          }
+          assayAverage = (float)Math.exp(sum/dataSize);       
+        }
+        else
+        {
+          for (Normalizable d : data)
+          {
+            sum = sum + d.getNormalizableData();            
+          }
+          assayAverage = (float)sum/dataSize;         
+        }
         scaleFactor = refValue / assayAverage;