Changeset 1074
 Timestamp:
 May 15, 2009, 2:38:58 PM (13 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
r1065 r1074 6 6 plugin set is a compilation of normalisers for expression data. See 7 7 ``Documentation`` below for further information about the different 8 plugins in this package. Common to the plugins provided with this9 package is that they work on bioassay set with either 1channel or 10 2channel. The algorithms are working on expression values, that is 11 for 2channel data, ratiosch1/ch2 are used.8 plugins in this package. Common to most of the plugins provided with 9 this package is that they work on bioassay sets with either 1channel 10 and 2channel data. The algorithms are working on expression values, 11 that is for 2channel data, ratio ch1/ch2 are used. 12 12 13 13 `Normalization package for BASE` is free software. See the file … … 50 50 == qQuantile normalization == 51 51 52 Write me. 52 The current implementation of qQuantile normalization supports only 53 1channel arrays. 53 54 54 55 The qQuantile normalization is inspired by the 'Cubic Spline' 55 56 normalization in Illumina Beadstudio and the work by Workman et al., 56 57 http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12225587 58 59 In qQuantile normalization, all assays (including the target) are 60 sorted in increasing intensity. The sorted list of probe intensities 61 are partitioned into q groups, and each of theses q groups are 62 adjusted (normalized) with the corresponding target group. After 63 normalization the intensity distribution of each assay will be 64 approximately the same as the target distribution. q is calculated as 65 q=max(10,min(100,target_size/10)). The program will stop if the number 66 of well defined expression values in the target or any of the assays 67 in the set is smaller than q. 68 69 The target is defined by selecting a subset of the assays in the 70 bioassay set, and the target expression values are the medians of 71 probe intensities over the bioassay set. Probes with no well defined 72 measurements in the bioassay set are simply ignored in target 73 calculation. 74 75 Since the normalization calculations are based on geometric means and 76 performed in log space the intensities must be positive and larger 77 than 0. Rather than expecting the user of qQuantile normalization to 78 remove such intensity the underlying algorithm silently ignores zero 79 and negative intensities. 80 81 Background subtraction and proper filtration should be done on the 82 bioassay set before running this plugin. 57 83 58 84 
plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/qQuantileNormalization.java
r1064 r1074 78 78 ( 79 79 "qQuantile normalization", 80 "In qquantile normalization ... Assays are not mixed.\n\n" + 81 "Background subtraction and proper filtration have to be done on the " + 80 "The qQuantile normalization is inspired by the 'Cubic Spline' " + 81 "normalization in Illumina Beadstudio and the work by Workman et al., " + 82 "http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12225587\n\n" + 83 "In qQuantile normalization, all assays (including the target) are " + 84 "sorted in increasing intensity. The sorted list of probe intensities " + 85 "are partitioned into q groups, and each of theses q groups are " + 86 "adjusted (normalized) with the corresponding target group. After " + 87 "normalization the intensity distribution of each assay will be " + 88 "approximately the same as the target distribution. q is calculated " + 89 "as q=max(10,min(100,target_size/10)). The program will stop if the " + 90 "number of well defined expression values in the target or any of the " + 91 "assays in the set is smaller than q.\n\n" + 92 "The target is defined by selecting a subset of the assays in the " + 93 "bioassay set, and the target expression values are the medians of " + 94 "probe intensities over the bioassay set. Probes with no well defined " + 95 "measurements in the bioassay set are simply ignored in target " + 96 "calculation.\n\n" + 97 "Since the normalization calculations are based on geometric means " + 98 "and performed in log space the intensities must be positive and " + 99 "larger than 0. Rather than expecting the user of qQuantile " + 100 "normalization to remove such intensity the underlying algorithm " + 101 "silently ignores zero and negative intensities.\n\n" + 102 "Background subtraction and proper filtration should be done on the " + 82 103 "bioassay set before running this plugin.\n\n" + 83 104 "Only 1channel data is supported\n\n" +
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