[909] | 1 | $Id: README 1087 2009-05-19 12:30:34Z martin $ |
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| 2 | |
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| 3 | = About `Normalization package for BASE` = |
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| 4 | |
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| 5 | The `Normalization package for BASE (net.sf.basedb.normalization)` |
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| 6 | plug-in set is a compilation of normalisers for expression data. See |
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| 7 | ``Documentation`` below for further information about the different |
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[1074] | 8 | plug-ins in this package. Common to most of the plug-ins provided with |
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| 9 | this package is that they work on bioassay sets with either 1-channel |
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| 10 | and 2-channel data. The algorithms are working on expression values, |
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| 11 | that is for 2-channel data, ratio ch1/ch2 are used. |
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[909] | 12 | |
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| 13 | `Normalization package for BASE` is free software. See the file |
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| 14 | license.txt for copying conditions. |
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| 15 | |
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[952] | 16 | The package was created, and is maintained, by Martin Svensson and |
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| 17 | Jari Hakkinen. |
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[909] | 18 | |
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| 19 | |
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| 20 | == Downloading == |
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| 21 | |
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| 22 | `Normalization package for BASE` can be obtained from |
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| 23 | |
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| 24 | http://baseplugins.thep.lu.se/wiki/PluginDownload |
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| 25 | |
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| 26 | |
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| 27 | = Installation = |
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| 28 | |
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| 29 | Installation instructions can be found in the 'INSTALL' file. |
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| 30 | |
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| 31 | |
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| 32 | = Documentation = |
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| 33 | |
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| 34 | |
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| 35 | == Average normalization == |
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| 36 | |
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[925] | 37 | This plug-in scales the expression values for an assay with a factor, |
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[928] | 38 | ''S'', equal to the ratio of either i) the geometric mean of the |
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| 39 | expression values of all spots in the bioassay set divided by the |
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| 40 | assay average, or ii) a user defined value divided by the assay |
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| 41 | average. |
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[909] | 42 | |
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[925] | 43 | The new expression values will become ''S'' times the original |
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| 44 | expression value. |
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[1087] | 45 | The user can choose between using geometric or arithmetic mean when |
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| 46 | calculating the averages. |
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[925] | 47 | |
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[909] | 48 | Background subtraction and proper filtration have to be done before |
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[925] | 49 | running this plug-in. |
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[909] | 50 | |
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| 51 | |
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[952] | 52 | == qQuantile normalization == |
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| 53 | |
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[1074] | 54 | The current implementation of qQuantile normalization supports only |
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| 55 | 1-channel arrays. |
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[952] | 56 | |
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| 57 | The qQuantile normalization is inspired by the 'Cubic Spline' |
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| 58 | normalization in Illumina Beadstudio and the work by Workman et al., |
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| 59 | http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12225587 |
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| 60 | |
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[1074] | 61 | In qQuantile normalization, all assays (including the target) are |
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| 62 | sorted in increasing intensity. The sorted list of probe intensities |
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| 63 | are partitioned into q groups, and each of theses q groups are |
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| 64 | adjusted (normalized) with the corresponding target group. After |
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| 65 | normalization the intensity distribution of each assay will be |
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| 66 | approximately the same as the target distribution. q is calculated as |
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| 67 | q=max(10,min(100,target_size/10)). The program will stop if the number |
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| 68 | of well defined expression values in the target or any of the assays |
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| 69 | in the set is smaller than q. |
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[952] | 70 | |
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[1074] | 71 | The target is defined by selecting a subset of the assays in the |
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| 72 | bioassay set, and the target expression values are the medians of |
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| 73 | probe intensities over the bioassay set. Probes with no well defined |
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| 74 | measurements in the bioassay set are simply ignored in target |
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| 75 | calculation. |
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| 76 | |
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| 77 | Since the normalization calculations are based on geometric means and |
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| 78 | performed in log space the intensities must be positive and larger |
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| 79 | than 0. Rather than expecting the user of qQuantile normalization to |
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| 80 | remove such intensity the underlying algorithm silently ignores zero |
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| 81 | and negative intensities. |
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| 82 | |
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| 83 | Background subtraction and proper filtration should be done on the |
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| 84 | bioassay set before running this plug-in. |
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| 85 | |
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| 86 | |
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[926] | 87 | == Quantile normalization == |
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[909] | 88 | |
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[926] | 89 | In quantile normalization each assay data is sorted in ascending |
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| 90 | expression value order and added to a matrix as columns. The matrix |
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| 91 | rows will contain mixed probes (also known as reporters or genes) |
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| 92 | decided by their rank. For each row in the matrix, the expression |
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| 93 | values are replaced with the row average value. Finally, each assay is |
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| 94 | reordered into its original order to retain a standard expression |
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| 95 | matrix were each row represents one probe. Assays are not mixed. |
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[909] | 96 | |
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[1051] | 97 | Background subtraction and proper filtration should be done on the |
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[909] | 98 | bioassay set before running this plug-in. The bioassay set must not |
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| 99 | contain any missing values. |
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| 100 | |
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[733] | 101 | ---------------------------------------------------------------------- |
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| 102 | {{{ |
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[909] | 103 | Copyright (C) 2008 Jari Häkkinen, Martin Svensson |
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[1051] | 104 | Copyright (C) 2009 Jari Häkkinen |
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[733] | 105 | |
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[909] | 106 | This file is part of the Normalizers plug-in package for BASE |
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| 107 | (net.sf.based.normalizers). The package is available at |
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| 108 | http://baseplugins.thep.lu.se/ BASE main site is |
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| 109 | http://base.thep.lu.se/ |
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[733] | 110 | |
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| 111 | This is free software; you can redistribute it and/or |
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| 112 | modify it under the terms of the GNU General Public License |
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[910] | 113 | as published by the Free Software Foundation; either version 3 |
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[733] | 114 | of the License, or (at your option) any later version. |
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| 115 | |
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| 116 | The software is distributed in the hope that it will be useful, |
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| 117 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 118 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 119 | GNU General Public License for more details. |
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| 120 | |
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| 121 | You should have received a copy of the GNU General Public License |
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[910] | 122 | along with this program. If not, see <http://www.gnu.org/licenses/>. |
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[733] | 123 | }}} |
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