Changeset 4308

Timestamp:

May 21, 2008, 10:49:43 PM (15 years ago)

Author:

Jari Häkkinen

Message:

Fixes #1030. User selects scaling/subtraction depending on whether data is log values or not.

File:

• branches/2.7-stable/src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java (modified) (9 diffs)

branches/2.7-stable/src/plugins/core/net/sf/basedb/plugins/MedianRatioNormalization.java

@@ -53 +53 @@
 import net.sf.basedb.core.RequestInformation;
 import net.sf.basedb.core.SpotBatcher;
+import net.sf.basedb.core.StringParameterType;
 import net.sf.basedb.core.Transformation;
 import net.sf.basedb.core.Type;
@@ -94 +95 @@
   (
     "Normalization: Median ratio",
-    ("This normalizer behaves differently depending on the array type.\n" +
-     "1-channel arrays: Intensities are translated such that resulting median is zero.\n" + 
+    ("This normalizer behaves differently depending on the array type.\n\n" +
+
+     "1-channel arrays: Intensities are changed in two different ways depending " +
+     "on user selection.\n" +
+     "a) For absolute intensity data the intensities should be scaled with the " +
+     "median intensity, Inew=Iold/Imedian, such that resulting median is 1.\n" +
+     "b) For log intensity data the intensities should be subtracted with the median " +
+     "intensity, log(Inew)=log(Iold)-log(Imedian), such that resulting median is 0.\n\n" + 
+
      "2-channel arrays: Intensities are scaled such " +
      "that their geometric mean (sqrt(i1 * i2)) is kept constant but " +
-     "the median of their ratios (i1/i2) is shifted to 1.\n" +
-     "All arrray types: The user can optionally exclude spots; all spots " +
+     "the median of their ratios (i1/i2) is shifted to 1.\n\n" +
+
+     "All array types: The user can optionally exclude spots; all spots " +
      "with at least one intensity below a user selectable threshold are " +
      "removed. User selectable (low/high intensity) fractions of the " +
@@ -138 +147 @@
     new FloatParameterType(0F, 100F, 5F, true)
   );
-  
+
+  /**
+     List of median normalization methods.
+
+     The method to use depends whether data is log values or
+     not. Absolute intensities should be scaled with the median
+     whereas log intensities should be subtracted with the median
+     intensity.
+
+       Inew = Iold/Imedian for absolute intensities.
+
+       log(Inew) = log(Iold) - log(Imedian) for log intensities.
+
+     Used with 1-channel data only
+  */
+  private static final
+  PluginParameter<String> methodParameter = new PluginParameter<String>
+    ( "method",
+      "Normalization method",
+      "Scale: Scaling of intensities, Inew=Iold/Imedian. Use with absolute intensities.\n" +
+      "Subtract: Subtraction of intensities, log(Inew)=log(Iold)-log(Imedian), Use with " +
+      "log intensities.",
+      new StringParameterType(255, "Scale", true, 1, 0, 0,
+                              Arrays.asList(
+                                new String[] { "Scale" ,
+                                               "Subtract" }
+                                )
+        )
+      );
+
+  /**
+     Used with 2-channel data only
+   */
   private static final PluginParameter<Integer> blockGroupParameter = new PluginParameter<Integer>
   (
@@ -226 +267 @@
         {
             case 1:
+              String method = (String) job.getValue(methodParameter.getName());
               normalize1ch(dc, source, batcher, minIntensity, lowExclude,
-                           highExclude, progress);
+                           highExclude, method.equals("Scale"), progress);
               break;
             case 2:
@@ -332 +374 @@
         storeValue(job, request, highExcludeParameter);
         storeValue(job, request, lowExcludeParameter);
+        // 1-channel only
+        storeValue(job, request, methodParameter);
         // 2-channel only
         storeValue(job, request, blockGroupParameter);
@@ -365 +409 @@
     @param highExclude A percentage of the spots with highest ratio
       that are excluded in the median calculation
+    @param scale If true, scale intensities with median intensity,
+      otherwise subtract median intensity
     @param progress Progress reporter for the caller to keep track of
     the plugin's progress. Null is allowed.
@@ -373 +419 @@
   normalize1ch(DbControl dc, BioAssaySet source, SpotBatcher batcher,
                float minIntensity, float lowExclude, float highExclude,
-               ProgressReporter progress)
+               boolean scale, ProgressReporter progress)
   {
     // Expressions used to get data
@@ -444 +490 @@
         for (int i = 0; i<nofChildSpots; ++i)
         {
-          batcher.insert(bioassayColumn, position[i], intensity[i]-median);
+          batcher.insert(bioassayColumn, position[i],
+                         (scale ? intensity[i]/median : intensity[i]-median) );
         }
         normalizedSpots += nofChildSpots;
@@ -647 +694 @@
         parameters.add(highExcludeParameter);
         parameters.add(lowExcludeParameter);
-        String description="Set minimum intensity, low exclude and high exclude";
-        if (nofChannels == 2)
+        String description="Set minimum intensity, low exclude, high exclude, and select method";
+        if (nofChannels == 1) {
+          parameters.add(methodParameter);
+        }
+        else if (nofChannels == 2)
         {
           parameters.add(blockGroupParameter);