Changeset 197

Timestamp:

Nov 21, 2006, 1:53:52 PM (16 years ago)

Author:

Johan Enell

Message:

callculates with good acc

Location:

trunk/se/lu/onk/ZTest/src/ztest

Files:

• Reporter.java (modified) (2 diffs)
• Spot.java (modified) (1 diff)
• Start.java (modified) (2 diffs)
• ZTest.java (modified) (7 diffs)

trunk/se/lu/onk/ZTest/src/ztest/Reporter.java

@@ -30 +30 @@
   private double m;
   private double p;
+  private int size;
   
   
@@ -61 +62 @@
     return m;
   }
+
+  public void setSize(int size)
+  {
+    this.size = size;
+  }
+
+  public int getSize()
+  {
+    return size;
+  }
 }

trunk/se/lu/onk/ZTest/src/ztest/Spot.java

@@ -26 +26 @@
 public class Spot
 {
-  float m;
+  double m;
   
-  public Spot(float m)
+  public Spot(Double m)
   {
     this.m = m;
   }
 
-  public final float getM()
+  public final double getM()
   {
     return m;
   }
 
+  @Override
+  public String toString()
+  {
+    return "["+m+"]";
+  }
+
   
 }

trunk/se/lu/onk/ZTest/src/ztest/Start.java

@@ -73 +73 @@
         {
           int index = mCol + i * assayFields.size();
-          float m = Float.NaN;
+          Double m = Double.NaN;
           if (!data[index].equals(""))
           {
-            m = new Float(data[index]);
+            m = new Double(data[index]);
           }
           spots[i] = new Spot(m);
@@ -130 +130 @@
       out.println("<meta http-equiv=\"Content-Type\" content=\"text/html; charset=ISO-8859-1\" />");
       out.println("<title>BASE 1.2.16dev - Experiment Enell:Enell Plugin</title>");
+      out.println("<link rel=\"stylesheet\" type=\"text/css\" href=\"base.css\" />");
       out.println("</head>");
       out.println("<table>");
-      out.println("<tr><th>Reporter</th><th>M</th><th>p</th><th>Rank</th><th>Number of expected</th><th>Ratio between expected and observed</th></tr>");
+      out.println("<tr><th>Reporter</th><th>Average M</th><th>P</th><th>Number of values</th><th>Rank</th<th>Expected</th><th>FDR</th></tr>");
+      
       for (int i = 0; i < bfss.getReporterSize() && i < 100; i++)
       {
+        int rank = i + 1;
         Reporter r = bfss.getReporter(i);
-        int numExpected = (int) (r.getP() * numOfReporters);
-        double ratio = numExpected / (i + 1.0);
-
-        out.print("<tr>");
+        double numExpected = r.getP() * numOfReporters;
+        double fdr = (numExpected / rank);
+        
+        out.print("<tr class=\"row"+(i%2+1)+"\">");
         out.printf(
-          "<td>%1$d</td><td>%2$g</td><td>%3$g</td><td>%4$d</td><td>%5$d</td><td>%6$g</td>",
+          "<td>%d</td>" +
+          "<td>%f</td>" +
+          "<td>%f</td>" +
+          "<td>%d</td>" +
+          "<td>%d</td>" +
+          "<td>%f</td>" +
+          "<td>%.2f</td>",
           r.getReporter(),
           r.getM(),
           r.getP(),
-          i + 1,
+          r.getSize(),
+          rank,
           numExpected,
-          ratio);
+          fdr);
         out.println("</tr>");
       }

trunk/se/lu/onk/ZTest/src/ztest/ZTest.java

@@ -24 +24 @@
 package ztest;
 
-import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
@@ -32 +31 @@
 public class ZTest
 {
-
+  private int precision = (int) Math.pow(10, 6);
+  
+  private int depth = 6;
+  
+  private double[] normsdistV;
+  
   public void calculate(BASEFileSpotSection<Reporter, Spot> bfss)
   {
+    normsdistV = new double[(precision * depth) + 1];
     List<Integer> assays = bfss.findFieldIntList("assays");
-    HashMap<Integer, Float> means = getAssayMeans(bfss, assays);
-    HashMap<Integer, Float> sds = getAssaySDS(bfss, assays, means);
-
+    HashMap<Integer, Double> means = getAssayMeans(bfss, assays);
+    HashMap<Integer, Double> sds = getAssaySDS(bfss, assays, means);
+    
+    fillNormsdist();
+    
     for (int i = 0; i < bfss.getReporterSize(); i++)
     {
@@ -48 +55 @@
       for (int j = 0; j < assays.size(); j++)
       {
-        double m = bfss.getSpot(i + j).getM();
+        double m = bfss.getSpot((i*assays.size()) + j).getM();
         if (!Double.isNaN(m))
         {
@@ -57 +64 @@
         }
       }
-      popSD = popSD / popSize;
+      popSD = Math.sqrt(popSD) / popSize;
       popMean = popMean / popSize;
       meanM = meanM / popSize;
 
       double z = z(meanM, popMean, popSD);
+      
       double normsdist = normsdist(Math.abs(z));
       double p = p(normsdist);
-      
-      bfss.getReporter(i).setP(p);
-      bfss.getReporter(i).setM(meanM);
+
+      Reporter r = bfss.getReporter(i); 
+      r.setP(p);
+      r.setM(meanM);
+      r.setSize(popSize);
     }
   }
@@ -72 +82 @@
   private double p(double normsdist)
   {
-    return 2 * (1 / normsdist);
+    return 2 * (1 - normsdist);
   }
 
   private double normsdist(double z)
   {
-    return 1 / Math.sqrt(2 * Math.PI) * Math.pow(Math.E, -0.5 * Math.pow(z, 2));
+    int zz = (int) Math.abs(Math.round(z * precision));
+    double value;
+    if (z < 0) throw new IllegalArgumentException("normsdist cant handle a negative z score");
+    else if (z <= (depth - 1)) value = normsdistV[zz];
+    else 
+    {
+      value = 1;
+    }
+    return value;
+  }
+  
+  private double distribution(double t)
+  {
+    return Math.pow(Math.E, -0.5 * Math.pow(t, 2)) / Math.sqrt(2 * Math.PI);
   }
 
@@ -84 +107 @@
     return (x - popMean) / popSD;
   }
+  
+  private void fillNormsdist()
+  {
+    normsdistV[0] = 0.5;
+    for (int i = 0; i < normsdistV.length-1; i++)
+    {
+      double w = (double)i/precision;
+      normsdistV[i+1] = normsdistV[i] + distribution(w)/precision;
+    }
+  }
 
-  private HashMap<Integer, Float> getAssaySDS(BASEFileSpotSection<Reporter, Spot> bfss, List<Integer> assays, HashMap<Integer, Float> means)
+  private HashMap<Integer, Double> getAssaySDS(BASEFileSpotSection<Reporter, Spot> bfss, List<Integer> assays, HashMap<Integer, Double> means)
   {
-    int[] size = new int[assays.size()];
-    float[] sqrSum = new float[assays.size()];
-    Arrays.fill(sqrSum, 0);
-
-    int count = bfss.findIntOpt("count");
-    for (int i = 0; i < count; i += assays.size())
+    HashMap<Integer, Double> sds = new HashMap<Integer, Double>();
+    for (int i = 0; i < assays.size(); i++)
     {
-      for (int j = 0; j < assays.size(); j++)
+      int size = 0;
+      double sqrSum = 0;
+      for (int j = 0; j < bfss.getSpotSize(); j += assays.size())
       {
-        float m = bfss.getSpot(i + j).getM();
-        if (!Float.isNaN(m))
+        double m = bfss.getSpot(i + j).getM();
+        if (!Double.isNaN(m))
         {
-          sqrSum[j] += Math.pow(m - means.get(assays.get(j)), 2);
-          size[j]++;
+          sqrSum += Math.pow(m - means.get(assays.get(i)), 2);
+          size++;
         }
       }
-    }
-    HashMap<Integer, Float> sds = new HashMap<Integer, Float>();
-    for (int i = 0; i < assays.size(); i++)
-    {
-      sds.put(assays.get(i), sqrSum[i] / size[i]);
+      sds.put(assays.get(i), Math.sqrt(sqrSum / size));
     }
 
@@ -113 +140 @@
   }
 
-  private HashMap<Integer, Float> getAssayMeans(BASEFileSpotSection<Reporter, Spot> bfss, List<Integer> assays)
+  private HashMap<Integer, Double> getAssayMeans(BASEFileSpotSection<Reporter, Spot> bfss, List<Integer> assays)
   {
-    int[] size = new int[assays.size()];
-    float[] sum = new float[assays.size()];
-    Arrays.fill(sum, 0);
-
-    int count = bfss.findIntOpt("count");
-    for (int i = 0; i < count; i += assays.size())
+    HashMap<Integer, Double> means = new HashMap<Integer, Double>();
+    for (int i = 0; i < assays.size(); i++)
     {
-      for (int j = 0; j < assays.size(); j++)
+      int size = 0;
+      double sum = 0;
+      for (int j = 0; j < bfss.getSpotSize(); j += assays.size())
       {
-        float m = bfss.getSpot(i + j).getM();
-        if (!Float.isNaN(m))
+        double m = bfss.getSpot(i + j).getM();
+        if (!Double.isNaN(m))
         {
-          sum[j] += m;
-          size[j]++;
+          sum += m;
+          size++;
         }
       }
+      means.put(assays.get(i), sum / size);
     }
-    HashMap<Integer, Float> means = new HashMap<Integer, Float>();
-    for (int i = 0; i < assays.size(); i++)
-    {
-      means.put(assays.get(i), sum[i] / size[i]);
-    }
-
     return means;
   }