Changeset 811


Ignore:
Timestamp:
Nov 11, 2008, 9:18:54 AM (13 years ago)
Author:
Martin Svensson
Message:

Fixes #141 Rank invariant should not support configurations. The plugin always returns false from now on. Also update the README file with some information about the Rank invariant plugin and AverageNorm?. plugin.

Location:
plugins/base2/net.sf.basedb.normalizers/trunk
Files:
2 edited

Legend:

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

    r747 r811  
    3232This README file contains general information about the normalization package
    3333and specific information about each algorithm used in the plug-ins. Installation
    34 instructions can be found in the INSTALL file.
     34instructions can be found in the INSTALL file.[[BR]]
     35These plug-ins work on bioassay set with either 1-channel or 2-channel data.
     36
    3537
    3638== Average normalization ==
    3739
     40This plug-in scales the intensities with a factor equal to the ratio of either
     41average intensity of all spots or user defined value to the average intensity of the given sample.[[BR]]
     42Background subtraction and proper filtration have to be done before running this plug-in.[[BR]]
    3843
    3944
     
    4449== Rank invariant normalization ==
    4550
    46 No plug-in supports this yet
    47 
     51With this plug-in the intensities for each assay is first ranked in an ascending order and then
     52a row-average over the assays is calculated for each row.
     53The sorted intensities are there after replaced by the corresponding row-average in the new child-bioassay set.[[BR]]
     54Background subtraction and proper filtration have to be done on the bioassay-set before running this plug-in.[[BR]]
  • plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/RankInvariantNormalization.java

    r755 r811  
    121121    return about;
    122122  }
    123 
     123  @Override
     124  public boolean supportsConfigurations()
     125  {
     126    return false;
     127  }
    124128  @Override
    125129  public void run(Request request, Response response,
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