Changeset 2167

Timestamp:

Dec 10, 2013, 9:50:53 AM (10 years ago)

Author:

olle

Message:

Refs #541. Rank invariant normalization updated to store data in same format as before the normalization, untransformed, log-2, log-10. (Note that Rank inveriant normalization currently is only implemented for one-channel data):

1. Class/file RankInvariantNormalization.java in src/net/sf/basedb/plugins/ in package net.sf.basedb.normalizers updated in private method BioAssaySet normalize1Ch(DbControl dc, BioAssaySet source, List<?> masterAssays, int numIteration, Job job, 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/RankInvariantNormalization.java (modified) (3 diffs)

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

@@ -31 +31 @@
 import net.sf.basedb.core.DynamicResultIterator;
 import net.sf.basedb.core.DynamicSpotQuery;
+import net.sf.basedb.core.IntensityTransform;
 import net.sf.basedb.core.ItemParameterType;
 import net.sf.basedb.core.Job;
@@ -299 +300 @@
     long numSpots;
     long normalizedSpots = 0;
+    IntensityTransform transform = source.getIntensityTransform();
     
     // Create Transformation
@@ -388 +390 @@
         List<Double> weights = getBiSquareWeights(rankInvSampleGenes, spot.getNormalizableData());
         double[] km = getNormCoeffs(rankInvMasterGenes, rankInvSampleGenes, weights);
-        float newIntensity = new Float((spot.getNormalizableData()-km[1]) / km[0]); 
-        
-        batcher.insert(bioassayColumn, spot.getPosition(), newIntensity);       
-      }
+        float newIntensity = new Float((spot.getNormalizableData()-km[1]) / km[0]);
+        // Normalization is calculated for untransformed data, transform channel data before storing
+        float transformedNewIntensity = 0F;
+        if (!Float.isNaN(newIntensity) && !Float.isInfinite(newIntensity))
+        {
+          transformedNewIntensity = (float) transform.transform(newIntensity);
+        }       
+        batcher.insert(bioassayColumn, spot.getPosition(), transformedNewIntensity);        
+      }
+      child.setIntensityTransform(transform);
       normalizedSpots += rankInvSampleGenes.size();     
     }