Changeset 2173


Ignore:
Timestamp:
Dec 12, 2013, 10:30:30 AM (7 years ago)
Author:
Jari Häkkinen
Message:

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

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

Legend:

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

    r1177 r2173  
    8181and negative intensities.
    8282
    83 The bioassay set to be normalized must be non-logged values since this
     83The bioassay set to be normalized must be non-logarithmic values since this
    8484plug-in will log all values before performing the normalization.
    8585
     
    9494rows will contain mixed probes (also known as reporters or genes)
    9595decided by their rank. For each row in the matrix, the expression
    96 values are replaced with the row average value. Finally, each assay is
     96values are replaced with the row average value (geometric or
     97arithmetic selectable by user). Finally, each assay is
    9798reordered into its original order to retain a standard expression
    9899matrix were each row represents one probe. Assays are not mixed.
     
    101102bioassay set before running this plug-in. The bioassay set must not
    102103contain any missing values.
     104
     105
    103106
    104107----------------------------------------------------------------------
  • plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/AbstractNormalizationPlugin.java

    r2165 r2173  
    7171    "averageMethod",
    7272    "Average calculation method",
    73     "Select which method to use when calculating averages.",
     73    "Select which method to use when calculating averages.\n" +
     74    "The selected average method is applied on non-logarithmic values. If input data " +
     75    "is marked as logarithmic in the input bioassay set then data is transformed to " +
     76    "non-logarithmic values before averaging with the selected method.",
    7477    null
    7578  ); 
Note: See TracChangeset for help on using the changeset viewer.