Changeset 1144

Timestamp:

Jul 29, 2009, 9:21:24 AM (14 years ago)

Author:

Martin Svensson

Message:

References #228 Updated the method that calculates bioassayset's global average in AverageNormalizationPlugin?, to support userdefine average method. Documentation related to recent changes has also been updated. The updated plugins execute as expected but the normalized data has not yet been verified.

Location:

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

Files:

• AbstractNormalizationPlugin.java (modified) (1 diff)
• AverageNormalization.java (modified) (8 diffs)
• QuantileNormalization.java (modified) (1 diff)

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

@@ -71 +71 @@
     "averageMethod",
     "Average calculation method",
-    "Select which method to use when calculating the averages.\n" +
-    "Geometric mean is default for none-logged values and arithmetic " +
+    "Select which method to use when calculating averages.\n" +
+    geometricOption +
+    " is default for none-logged values and " + arithmeticOption +
     "is default for logged values.",
     null

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

@@ -69 +69 @@
 /**
    This plug-in scales the expression values for an assay with a
-   factor, ''S'', equal to the ratio of either i) the geometric mean
+   factor, ''S'', equal to the ratio of either i) the mean
    of the expression values of all spots in the bioassay set divided
    by the assay average, or ii) a user defined value divided by the
-   assay average.
+   assay average. Which average method to use is selected in the job
+   configuration process. 
 
    The new expression values will become ''S'' times the original
    expression value.
 
-   Background subtraction and proper filtration have to be done before
-   running this plug-in.
+   Background subtraction and proper filtration should be done on the
+   bioassay set before running this plug-in.
   
    @author Martin
@@ -106 +107 @@
     (
       "useGlobalAvgInt", 
-      "Use global geometric mean intensity",
-      "Select if the global geometric mean intensity or an user defined value should be used as a reference value\n" +
-      noOption + " = User defined value(default)\n" +
-      yesOption + " = Global geometric mean intensity",
+      "Use global mean intensity",
+      "Select if the global mean intensity should be used as a reference value.\n" +
+      noOption + " = User defined reference value is used(default).\n" +
+      yesOption + " = Global mean intensity is used.",
       new StringParameterType(null, noOption, true, 1, 0, 0, Arrays.asList(new String[] {noOption, yesOption}))
     ); 
@@ -121 +122 @@
     "Reference value",
     "Reference value to use when calculating the scaling factor. Default value is 100\n" +
-    "This parameter cannot be null if 'Use global geometric mean intensity' is " + noOption + ".",
+    "This parameter cannot be null if 'Use global mean intensity' is " + noOption + ".",
     new FloatParameterType(null, null, 100f, false)
   );
@@ -304 +305 @@
         if (useGlobalAvgInt)
         { 
-          refValue = getGlobalGeometricMeanIntensity(dc, source, minIntensity, (String)job.getValue("averageMethod"));
+          refValue = getGlobalMeanIntensity(dc, source, minIntensity, (String)job.getValue("averageMethod"));
         }
         else
@@ -515 +516 @@
         if (progress != null)
           progress.display((int)((100L * normalizedSpots) / numSpots),
-                           normalizedSpots + " spots normalized");
+                           normalizedSpots + " spots processed");
       }
       batcher.flush();
@@ -530 +531 @@
     either 1-channel or 2-channel data.
    */
-  private float getGlobalGeometricMeanIntensity(DbControl dc, BioAssaySet source, float minIntensity, String averageMethod)
+  private float getGlobalMeanIntensity(DbControl dc, BioAssaySet source, float minIntensity, String averageMethod)
     throws SQLException, BaseException
   {
@@ -546 +547 @@
       break;
     case 2:
-      ratio = Expressions.ln(Expressions.divide(ch1, ch2));
+      ratio = Expressions.divide(ch1, ch2);
       break;
     default:
       throw new BaseException(noOfChannels + " channel-data is not supported by this plugin");
-    }   
-    
+    }       
         
     if (arithmeticOption.equals(averageMethod)) mean = Aggregations.mean(ratio);
@@ -565 +565 @@
     else throw new BaseException("The global average intensity could not be calculated");
     
-    return (float)Math.exp(meanValue);
+    return (float)meanValue;
   }
 }

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

@@ -319 +319 @@
   private BioAssaySet normalize(DbControl dc, BioAssaySet source,
       Job job, ProgressReporter progress)
-  {
-    String averageMethod = (String)(job.getParameterValue("averageMethod"));
-    
+  { 
     int noOfChannels = source.getRawDataType().getChannels();
     long normalizedSpots = 0;