Changeset 1044

Timestamp:

Apr 23, 2009, 7:09:51 PM (14 years ago)

Author:

Jari Häkkinen

Message:

Addresses #118 and #206. If no assay data is given use the average of all assays as reference ... fixed create_target for this case.

File:

• plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc (modified) (2 diffs)

plugins/base2/net.sf.basedb.normalizers/trunk/src/c++/bin/qQN.cc

@@ -56 +56 @@
 {
   CommandLine cmd;
-  OptionInFile assay(cmd, "assay-data", "assay annotations", true);
+  OptionInFile assay(cmd, "assay-data", "assay annotations");
   OptionInFile indata(cmd, "in-data", "data to be normalized");
   OptionOutFile outdata(cmd, "out-data", "normalized data");
@@ -159 +159 @@
   for (size_t row=0; row<m.rows(); ++row) {
     t[row]=0;
+    size_t column_contribs=0;
     for (size_t column=0; column<m.columns(); ++column)
-      t[row]+=m(row,column).data();
-    t[row]/=m.columns();
+      if (m(row,column).weight()) { // weight either 0 or 1
+        t[row]+=m(row,column).data();
+        ++column_contribs;
+      }
+    if (!column_contribs)
+      throw std::runtime_error("At least one row with no valid reference");
+    t[row]/=column_contribs;
   }
 }