Changeset 1203


Ignore:
Timestamp:
Mar 11, 2010, 11:30:14 AM (12 years ago)
Author:
Jari Häkkinen
Message:

Improved documentation for Background correction plug-in

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

Legend:

Unmodified
Added
Removed
  • plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails

    r1197 r1203  
    55There are many plug-ins in the Illumina plug-in package for BASE. This
    66file gives detailed information on some of the contributed plug-ins.
     7
     8
     9== Illumina expression background correction plug-in ==
     10
     11This plug-in will remove a per-slide global background from all
     12spots. The background is calculated from a set of negative control
     13spot on the array. See implementation details below for details.
     14
     15=== Parameters ===
     16
     17The only parameter to set is how background intensities should be
     18calculated. Allowed values are median or mean, i.e. the background is
     19either the median or the mean of the negative control spots on the
     20array.
     21
     22=== Implementation details ===
     23
     24Each assay is treated separately, i.e., no samples are combined
     25together. All calculations are made on the current bioassay data
     26implying that this plug-in should be used early in analysis and before
     27background spots are removed.
     28
     29A spot is considered to be a negative control spot if it has an
     30''Control group name'' exactly matching the string ''negative''.
     31
    732
    833
     
    2550plug-in.
    2651
    27 
    2852=== Parameters ===
    2953
     
    4266}}}
    4367where `MAD` is the median absolute deviation.
    44 
    4568
    4669=== Implementation details ===
     
    7093value for arguments outside this range is set to -1 and 1,
    7194respectively.
     95
    7296
    7397
     
    100124----------------------------------------------------------------------
    101125{{{
    102 Copyright (C) 2009 Jari Häkkinen
     126Copyright (C) 2009, 2010 Jari Häkkinen
    103127
    104128This file is part of Illumina plug-in package for BASE.
  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BackgroundCorrection.java

    r1120 r1203  
    9191  private static final About about = new AboutImpl
    9292    ( "Illumina expression background correction",
    93       "This plug-in implements BeadStudio like background correction methods " +
    94       "for Illumina expression data. Please send feedback to " +
     93      "This plug-in will remove a per-slide global background from all " +
     94      "spots. The background is calculated from a set of negative control " +
     95      "spots on the array.\n\n" +
     96      "Each assay is treated separately, i.e., no samples are combined " +
     97      "together. All calculations are made on the current bioassay data " +
     98      "implying that this plug-in should be used early in analysis and before " +
     99      "background spots are removed.\n\n" +
     100      "A spot is considered to be a negative control spot if it has an " +
     101      "''Control group name'' exactly matching the string ''negative''.\n\n" +
     102      "The only parameter to set is how background intensities should be " +
     103      "calculated. Allowed values are median or mean, i.e. the background is " +
     104      "either the median or the mean of the negative control spots on the " +
     105      "array.\n\n" +
     106      "Please send feedback to " +
    95107      Illumina.EMAIL,
    96108      Illumina.VERSION,
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