Changeset 2173
 Timestamp:
 Dec 12, 2013, 10:30:30 AM (7 years ago)
 Location:
 plugins/base2/net.sf.basedb.normalizers/trunk
 Files:

 2 edited
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plugins/base2/net.sf.basedb.normalizers/trunk/README
r1177 r2173 81 81 and negative intensities. 82 82 83 The bioassay set to be normalized must be nonlog gedvalues since this83 The bioassay set to be normalized must be nonlogarithmic values since this 84 84 plugin will log all values before performing the normalization. 85 85 … … 94 94 rows will contain mixed probes (also known as reporters or genes) 95 95 decided by their rank. For each row in the matrix, the expression 96 values are replaced with the row average value. Finally, each assay is 96 values are replaced with the row average value (geometric or 97 arithmetic selectable by user). Finally, each assay is 97 98 reordered into its original order to retain a standard expression 98 99 matrix were each row represents one probe. Assays are not mixed. … … 101 102 bioassay set before running this plugin. The bioassay set must not 102 103 contain any missing values. 104 105 103 106 104 107  
plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/AbstractNormalizationPlugin.java
r2165 r2173 71 71 "averageMethod", 72 72 "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 nonlogarithmic values. If input data " + 75 "is marked as logarithmic in the input bioassay set then data is transformed to " + 76 "nonlogarithmic values before averaging with the selected method.", 74 77 null 75 78 );
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