Changeset 975

Timestamp:

Feb 26, 2009, 12:13:51 PM (15 years ago)

Author:

Martin Svensson

Message:

References #119 Some changes in the calculation-part. The plug-in runs through but the result has not been verified.

Location:

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

Files:

• AbstractNormalizationPlugin.java (modified) (1 diff)
• RankInvariantNormalization.java (modified) (10 diffs)

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

@@ -165 +165 @@
       // Load spot data for this bioassay
       short bioassayColumn = assay.getDataCubeColumnNo();
+      if (!query.getParameterNames().contains("bioAssayColumn"))
+      {
+        // Create restriction: column = :bioAssayColumn
+        Restriction bioAssayRestriction = Restrictions.eq(
+            Dynamic.column(VirtualColumn.COLUMN), 
+            Expressions.parameter("bioAssayColumn")
+          );
+        query.restrict(bioAssayRestriction);
+      }
       query.setParameter("bioAssayColumn", (int)bioassayColumn, Type.INT);
       DynamicResultIterator it = query.iterate(dc);

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

@@ -39 +39 @@
 import net.sf.basedb.core.Transformation;
 import net.sf.basedb.core.Type;
+import net.sf.basedb.core.VirtualColumn;
 import net.sf.basedb.core.plugin.About;
 import net.sf.basedb.core.plugin.AboutImpl;
@@ -45 +46 @@
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
+import net.sf.basedb.core.query.Dynamic;
+import net.sf.basedb.core.query.Expressions;
+import net.sf.basedb.core.query.Restriction;
+import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.core.query.SqlResult;
 import net.sf.basedb.core.signal.SignalHandler;
@@ -130 +135 @@
     storeValue(job, request, ri.getParameter(CHILD_DESCRIPTION));
     
-    storeValue(job, request, ri.getParameter("masterSample"));
+    storeValues(job, request, ri.getParameter("masterSample"));
     storeValue(job, request, ri.getParameter("numIterations"));
     
@@ -286 +291 @@
         );
         parameters.add(masterSampleParameter);
-        // TODO Add parameter to set the number of iterations to get the least square fit?
-        
-        //TODO More parameters?
+    
         String description = "TODO";
         
@@ -334 +337 @@
     query.reset();
         
+    
+    // Create restriction: column = :bioAssayColumn
+    Restriction bioAssayRestriction = Restrictions.eq(
+        Dynamic.column(VirtualColumn.COLUMN), 
+        Expressions.parameter("bioAssayColumn")
+      );
+    query.restrictPermanent(bioAssayRestriction);
+    
     // Get spot data for the master sample
     if (progress != null) progress.display(0, "Calculate master sample");
@@ -343 +354 @@
     for (BioAssay assay : assays)
     {
+      // Update progress reporter
+      if(progress != null) progress.display(
+          (int)((100L * normalizedSpots)/numSpots), 
+        normalizedSpots + " spots normalized");
+      
       short bioassayColumn = assay.getDataCubeColumnNo();
       List<AbstractSpotData> data = getSpots(dc, assay, query, assay.getRawDataType().getChannels());
@@ -349 +365 @@
         
       // Pick out rank invariant genes from the highRank(90th percentile) and lowRank(50th-25th percentile).
-      float rankQuot = 0;
-      int highRankIndex = Math.round(((data.size() / 100)*highRank)+0.5f);
+      double rankQuot = 0.0;
+      int highRankIndex = Math.round(((data.size() / 100f)*highRank)+0.5f);
       int lowRankIndex;
       int decrLowRank = 0;
-      List<SpotData1Ch> rankInvSampleGenes;
-      List<Double> rankInvMasterGenes;
+      List<SpotData1Ch> rankInvSampleGenes = new ArrayList<SpotData1Ch>();
+      List<Double> rankInvMasterGenes = new ArrayList<Double>();
       // Iterate until at least 2% of the genes are considered to be rank invariant. 
       // LowRank is decreased with 5 steps each time.
-      do
-      {
-        rankInvSampleGenes  = new ArrayList<SpotData1Ch>();
+      while (rankQuot < 0.02f && ((lowRank-decrLowRank) >= 25))
+      {
+        lowRankIndex = Math.round(((data.size() / 100)*(lowRank-decrLowRank))+0.5f);
+
+        rankInvSampleGenes = new ArrayList<SpotData1Ch>();
         rankInvMasterGenes = new ArrayList<Double>();
-        
-        lowRankIndex = Math.round(((data.size() / 100)*(lowRank-decrLowRank))+0.5f);
-        
-        // Map<position, rank>    
-        Map<Integer, Integer> sampleRankMap = getRankedPositions(data, highRankIndex, lowRankIndex);        
-        Map<Integer, Integer> masterRankMap = getRankedPositions(masterSample, highRankIndex, lowRankIndex);
-        
-        for (int i=0; i < dataSize ; i++)
-        {           
-          AbstractSpotData d = data.get(i);
-          // Gets the gene's ranking in master and current sample
-          Integer masterRank = masterRankMap.get(d.getPosition());
-          Integer sampleRank = sampleRankMap.get(d.getPosition());
+        //Map<position, rank>
+        Map<Integer, Integer> sampleRanks = new HashMap<Integer, Integer>();
+        Map<Integer, Integer> masterRanks = new HashMap<Integer, Integer>();
+        
+        for (int i=lowRankIndex; i<=highRankIndex; i++)
+        {
+          sampleRanks.put(data.get(i).getPosition(), i);
+          masterRanks.put(masterSample.get(i).getPosition(), i);
           
-          // Check the relative rank between master and sample if 
-          //the position exists in both of them
-          if (masterRank != null && sampleRank != null)
+        }
+        for (Integer pos : sampleRanks.keySet())
+        {
+          Integer sRank = sampleRanks.get(pos);
+          Integer mRank = masterRanks.get(pos);
+          float distance = (sRank != null && mRank != null) ? Math.abs((sRank - mRank) / mRank) : 1f;
+          if (distance < 0.05)
           {
-            float div = (Math.abs(sampleRank-masterRank) / masterRank);
-            if (div < 0.05) 
-            {
-              rankInvSampleGenes.add((SpotData1Ch)d);
-              rankInvMasterGenes.add((double)masterSample.get(masterRank).getNormalizableData());
-            }
+            rankInvSampleGenes.add((SpotData1Ch)data.get(sRank));
+            rankInvMasterGenes.add((double)masterSample.get(mRank).getNormalizableData());
           }
-        }       
-        rankQuot = rankInvSampleGenes.size() / data.size();
+        } 
+        float numRankedGenes = rankInvSampleGenes.size();       
+        rankQuot = numRankedGenes / new Float(highRankIndex-lowRankIndex+1);
         decrLowRank += 5;
-      }while (rankQuot < 0.02 || (lowRank-decrLowRank) >= 25);
+      }
 
       for (SpotData1Ch spot : rankInvSampleGenes)
@@ -395 +409 @@
         List<Double> weights = getBiSquareWeights(rankInvSampleGenes, spot.getNormalizableData());
         double[] km = getNormCoeffs(rankInvMasterGenes, rankInvSampleGenes, weights);
-        float newCh1 = new Float((spot.getNormalizableData()-km[1]) / km[0]); 
-        
-        batcher.insert(bioassayColumn, spot.getPosition(), newCh1);       
-      }
-      normalizedSpots += rankInvSampleGenes.size();
-      
-      // Update progress reporter
-      if(progress != null) progress.display(
-          (int)((100L * normalizedSpots)/numSpots), 
-        normalizedSpots + " spots normalized");
+        float newIntensity = new Float((spot.getNormalizableData()-km[1]) / km[0]); 
+        
+        batcher.insert(bioassayColumn, spot.getPosition(), newIntensity);       
+      }
+      normalizedSpots += rankInvSampleGenes.size();     
     }
     batcher.flush();
@@ -410 +419 @@
     
     return child;
-  }
-
-  /*
-    Gets positions of those genes that are ranked between two values.
-    The data-parameter must be list sorted asc.
-   */
-  @SuppressWarnings("unchecked")
-  private Map<Integer, Integer> getRankedPositions(List<? extends AbstractSpotData> data, int highRankIndex, int lowRankIndex)
-  {   
-    Map<Integer, Integer> rankedPos = new HashMap<Integer, Integer>();
-    for (AbstractSpotData spd : data)
-    {
-      int dataIndex = data.indexOf(spd);
-      if (dataIndex <= highRankIndex && dataIndex >= lowRankIndex)
-      {
-        rankedPos.put(spd.getPosition(), data.indexOf(spd));
-      }
-    }
-    return rankedPos;
   }
 
@@ -440 +430 @@
     {
       BioAssay assay = (BioAssay)obj;
+      assay = BioAssay.getById(dc, assay.getId());
       try
       {