Changeset 2166

Timestamp:

Dec 9, 2013, 4:08:44 PM (9 years ago)

Author:

olle

Message:

Refs #228. Refs #541. Average normalization updated to untransform logarithmic data before normalization, and then transform it back to logarithmic format before results are stored. Default averaging method will always be set to Formula.AverageMethod.GEOMETRIC_MEAN:

1. Class/file AverageNormalization.java in src/net/sf/basedb/plugins/ in package net.sf.basedb.normalizers updates:
   a. Private method RequestInformation getConfiguredJobParameters() updated to always set the default averaging method to Formula.AverageMethod.GEOMETRIC_MEAN.
   b. Private method BioAssaySet normalize(DbControl dc, BioAssaySet source, Job job, float refValue, float minIntensity, ProgressReporter progress) updated to call public method double transform(double value) in class IntensityTransform to transform the normalized result back before storing it.

File:

• plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/AverageNormalization.java (modified) (3 diffs)

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

@@ -347 +347 @@
         parameters.add(getChildDescriptionParameter(null, null, null)); 
         // Average normalization options        
-        Formula.AverageMethod defaultAverageMethod = Formula.AverageMethod.ARITHMETIC_MEAN;
-        IntensityTransform transform = bas.getIntensityTransform();
-        if (transform == IntensityTransform.NONE)
-        {
-          defaultAverageMethod = Formula.AverageMethod.GEOMETRIC_MEAN;
-        }
+        // Default is always set to geometric mean, since averaging is performed on untransformed data 
+        Formula.AverageMethod defaultAverageMethod = Formula.AverageMethod.GEOMETRIC_MEAN;
         StringParameterType spt = new StringParameterType
         (
@@ -399 +395 @@
     long numSpots;
     long normalizedSpots = 0;
+    IntensityTransform transform = source.getIntensityTransform();
     
     // Create Transformation
@@ -489 +486 @@
         {
           d.setNormalizableData(scaleFactor * d.getNormalizableData());
-          batcher.insert(bioassayColumn, d.getPosition(), d.getChannelData());
+          // Average is calculated for untransformed data, transform channel data before storing
+          float[] channelDataArr = d.getChannelData();
+          float[] transformedChannelDataArr = new float[channelDataArr.length];
+          for (int i=0; i < channelDataArr.length; i++)
+          {
+            // d1 = untransormed value, d2 = transformed value (0 if d1 is out of range)
+            float d1 = channelDataArr[i];
+            float d2 = 0F;
+            if (!Float.isNaN(d1) && !Float.isInfinite(d1))
+            {
+              d2 = (float) transform.transform(d1);
+            }
+            transformedChannelDataArr[i] = d2;
+          }
+          batcher.insert(bioassayColumn, d.getPosition(), transformedChannelDataArr);
           normalizedSpots++;
         }
+        child.setIntensityTransform(transform);       
         if (progress != null)
           progress.display((int)((100L * normalizedSpots) / numSpots),