Changeset 2173

Timestamp:

Dec 12, 2013, 10:30:30 AM (10 years ago)

Author:

Jari Häkkinen

Message:

Refs #228 and #541. Improving doc and help string

Location:

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

Files:

• README (modified) (3 diffs)
• src/net/sf/basedb/plugins/AbstractNormalizationPlugin.java (modified) (1 diff)

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

@@ -81 +81 @@
 and negative intensities.
 
-The bioassay set to be normalized must be non-logged values since this
+The bioassay set to be normalized must be non-logarithmic values since this
 plug-in will log all values before performing the normalization.
 
@@ -94 +94 @@
 rows will contain mixed probes (also known as reporters or genes)
 decided by their rank. For each row in the matrix, the expression
-values are replaced with the row average value. Finally, each assay is
+values are replaced with the row average value (geometric or
+arithmetic selectable by user). Finally, each assay is
 reordered into its original order to retain a standard expression
 matrix were each row represents one probe. Assays are not mixed.
@@ -101 +102 @@
 bioassay set before running this plug-in. The bioassay set must not
 contain any missing values.
+
+
 
 ----------------------------------------------------------------------

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 averages.",
+    "Select which method to use when calculating averages.\n" +
+    "The selected average method is applied on non-logarithmic values. If input data " +
+    "is marked as logarithmic in the input bioassay set then data is transformed to " +
+    "non-logarithmic values before averaging with the selected method.",
     null
   );