Ticket #970: norm.export.xml

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE configfile SYSTEM "plugin-configuration-file.dtd"><configfile>
  <configuration pluginClassName="se.uu.lcb.plugins.PluginExecuter">
    <configname>Normalization: Within arrays</configname>
    <description>This plug-in normalizes log-ratios for each array individually by various methods for averaging log-ratios to zero within each array or sub-array. The print-tip version of this normalization, which is a local fitting of the regression line, is usually preferred since it corrects for both spatial effects and dye biases. All available methods are listed below:&#xD;
- Median: The median log-ratio is centered on zero.&#xD;
- Loess: All intensities on the array are fitted to a regression line, so that dye biases are removed. Yang et al (2001, 2002)&#xD;
- Print-tip loess: Loess normalization is perfromed within each sub array, so that both spatial effects and dye biases are removed. Yang et al (2001, 2002)&#xD;
- Composite: This method is not yet operational.&#xD;
- Robust spline: Robustly fitted regression splines and empirical Bayes shrinkage.</description>
    <parameter>
      <name>leaveStdin</name>
      <label>Leave stdin.txt</label>
      <description>If the file stdin.txt should be removed after the plug-in execution or not</description>
      <class>java.lang.Boolean</class>
      <value>false</value>
    </parameter>
    <parameter>
      <name>leaveStdout</name>
      <label>Leave stdout.txt</label>
      <description>If the file stdout.txt should be removed after the plug-in execution or not</description>
      <class>java.lang.Boolean</class>
      <value>false</value>
    </parameter>
    <parameter>
      <name>parameters</name>
      <label>Job parameters</label>
      <description>Job parameters</description>
      <class>java.lang.String</class>
      <value>fname\thidden\tnormalization.R\tfname</value>
      <value>norm.method\tenum\tprinttiploess;printtiploess|loess;loess|median;median|composite;composite|robustspline;robustspline\tNormalization method</value>
      <value>smooth.param\tfloat\t0.3\tProp. size of local regression moving window</value>
      <value>specifyLayout\tbool\ttrue\tSpecify array layout dimensions?</value>
      <value>ngrid.r.in\tint\t0\tGrid rows per slide</value>
      <value>ngrid.c.in\tint\t0\tGrid columns per slide</value>
      <value>nspot.r.in\tint\t0\tSpot rows per print-tip group</value>
      <value>nspot.c.in\tint\t0\tSpot columns per print-tip group</value>
      <value>use.weights\tbool\tfalse\tAssociate quality weights with flag values?</value>
      <value>weight.0\tfloat\t\tFlag values with weight 0</value>
      <value>weight.25\tfloat\t\tFlag values with weight 0.25</value>
      <value>weight.5\tfloat\tNA\tFlag values with weight 0.5</value>
      <value>weight.75\tfloat\tNA\tFlag values with weight 0.75</value>
      <value>debug.level\thidden\t0\tdebug.level</value>
    </parameter>
    <parameter>
      <name>usedFields</name>
      <label>Spot fields</label>
      <description>Spot fields</description>
      <class>java.lang.String</class>
      <value>intensity1</value>
      <value>intensity2</value>
      <value>raw.flags</value>
    </parameter>
    <parameter>
      <name>displayAssayOrder</name>
      <label>Display assay order</label>
      <description>Display assay order</description>
      <class>java.lang.Boolean</class>
      <value>false</value>
    </parameter>
    <parameter>
      <name>executablePath</name>
      <label>Path to executable</label>
      <description>Path to executable file</description>
      <class>java.lang.String</class>
      <value>/Sites/plugins/base1/bin</value>
    </parameter>
    <parameter>
      <name>isOneChannel</name>
      <label>One channel data</label>
      <description>One channel data</description>
      <class>java.lang.Boolean</class>
      <value>false</value>
    </parameter>
    <parameter>
      <name>usedColumns</name>
      <label>Reporter columns</label>
      <description>Reporter columns</description>
      <class>java.lang.String</class>
      <value>rep.position</value>
      <value>rep.id</value>
    </parameter>
    <parameter>
      <name>execName</name>
      <label>Name of executable</label>
      <description>Name of executable</description>
      <class>java.lang.String</class>
      <value>R2.pl</value>
    </parameter>
  </configuration>
</configfile>