Changeset 788 for plugins/base1/se.lu.onk.MergeBioAssay
- Timestamp:
- Sep 18, 2008, 11:02:25 PM (15 years ago)
- Location:
- plugins/base1/se.lu.onk.MergeBioAssay/trunk
- Files:
-
- 2 edited
Legend:
- Unmodified
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plugins/base1/se.lu.onk.MergeBioAssay/trunk/README
r776 r788 3 3 = About `se.lu.onk.MergeBioAssay` = 4 4 5 The `se.lu.onk.MergeBioAssay` plug-in for BASE is 5 The `se.lu.onk.MergeBioAssay` plug-in merge bioassays by grouping them 6 according to annotation types or syntactical differences in the 7 name. See ``Documentation`` below fo further information about the 8 plug-in. 6 9 7 10 `se.lu.onk.MergeBioAssay` is free software. See the file license.txt for … … 78 81 # wget http://baseplugins.thep.lu.se/.../BaseFile-1.0.tgz 79 82 # wget http://baseplugins.thep.lu.se/.../BaseFile-1.0.tgz.MD5 80 83 # optionally compare the MD5 sum of the downloaded file and the MD5-file 81 84 # tar zxpf BaseFile-1.0.tgz 82 85 # ln -s BaseFile-1.0 BaseFile … … 98 101 == Bug Reporting == 99 102 100 You can report `se.lu.onk.MergeBioAssay` bugs on 103 You can report `se.lu.onk.MergeBioAssay` bugs on 101 104 102 105 http://baseplugins.thep.lu.se/newticket … … 119 122 120 123 124 == Documentation == 125 126 This plug-in base-users merge bioassays by grouping them according to 127 annotation types or syntactical differences in the name. There are 128 four different methods for calculating the merged values. They differ 129 in what kind of mean they are using (arithmetic or geometric) and if 130 they are merging on ratio or intensity. 131 132 For each group the parents are saved so the link to the raw data is 133 preserved. Annotations for the bioassays are saved if sample1 is the 134 same for each assay in each group. 135 136 === Merge methods === 137 138 ''Geometric mean of ratio'':: 139 This method calculates the geometric mean of the ratios in each 140 group per position. 141 142 ''Arithmetic mean of ratio'':: 143 This method calculates the arithmetic mean of the ratios in each 144 group per position. 145 146 ''Arithmetic mean of intensity'':: 147 This method calculates the arithmetic mean of the intensities in 148 each group per position. 149 150 ''Ratio of ratio'':: 151 This method works a little bit different from the others. It 152 requires that each group consists of exactly two bioassays. It will 153 then create a new ratio for each spot with one of the assays over 154 the other, depending on what the user has specified in the ratio 155 parameters. 156 157 === Parameters === 158 159 ''Assayname'':: 160 This parameter specifies how the name of the assays is 161 constructed. Use %0-%9 as wildcards and then put any character(s) 162 between as delimiters. For example assay name Assay_1_A can be 163 divided into three parts. By setting the parameter to %1_%2_%3 the 164 plugin will read assay name assay_1_A and set %1=Assay, %2=1 and 165 %3=A. Thus, if your assays have names constructed in the same way 166 merge can sort the assays in groups depending on %1, %2 or %3. 167 168 ''Group'':: 169 This will specify how the assays will be grouped together. It can 170 either be a %-number used in assayname or an annotation type. 171 172 Example 1: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can 173 be sorted into groups of assays using merge. 174 175 A: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter 176 \221Group\222 = %2 will sort the assays into two groups. 177 {{{ 178 One group were %2=1 (assays Assay_1_A and Assay_1_B) 179 One group were %2=2 (assays Assay_2_A and Assay_2_B) 180 }}} 181 B: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter 182 \221Group\222 = %3 will sort the assays into two groups. 183 {{{ 184 One group were %3=A (assays Assay_1_A and Assay_2_A) 185 One group were %3=B (assays Assay_1_B and Assay_1_B) 186 }}} 187 188 ''New name'':: 189 This text will be used in the name of the merged assays. The name 190 will be this string followed by the groupname. 191 192 ''Merge method'':: 193 Choose one of the methodes described above. 194 195 ''Ratio'':: 196 If merge method `ratio of ratio` is chosen the form of the ratio 197 must be specified. This is done either in the ratio parameter or in 198 ratio annotation type and ratio annotation value. In the ratio 199 parameter you can choose a %-number followed by the two values it 200 can take. The last character in the string must be the delimiter the 201 user has choosen ot use. The other way a user can specify the ratio 202 is by choosing an annotation type in the list and specify the values 203 in the annotation values parameter. This is done by writing the 204 values with the delimiter used last, 205 {{{ 206 %1|vr1|vr2| 207 }}} 208 This will take the values from %1 in the assayname and put the assay 209 with value vr1 over the assay with values vr2. Notice that the final 210 character is the delimiter (this can of course be any character). 211 212 Example 2: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be 213 sorted into groups of assays using merge. 214 215 A: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter 216 \221Group\222 = %2 will sort the assays into two groups. 217 {{{ 218 One group were %2=1 (assays Assay_1_A and Assay_1_B) 219 One group were %2=2 (assays Assay_2_A and Assay_2_B) 220 }}} 221 B: By setting parameter \221Ratio\222 = %3|A|B| ratios of ratios 222 will be created as: 223 {{{ 224 Assay_1_A / Assay_1_B 225 Assay_2_A / Assay_2_B 226 }}} 227 228 === References === 229 230 [http://mathworld.wolfram.com/ArithmeticMean.html Arithmetic mean] [[br]] 231 [http://mathworld.wolfram.com/GeometricMean.html Geometric mean] 232 121 233 122 234 ---------------------------------------------------------------------- -
plugins/base1/se.lu.onk.MergeBioAssay/trunk/build.xml
r783 r788 1 1 <?xml version="1.0" encoding="UTF-8"?> 2 2 <!-- 3 3 $Id$ 4 4 5 6 5 Copyright (C) 2005, 2006 Johan Enell 6 Copyright (C) 2008 Jari Häkkinen 7 7 8 8 This file is part of the se.lu.onk.MergeBioAssay plug-in for 9 9 BASE. Available at http://baseplugins.thep.lu.se/ and BASE web 10 10 site is http://base.thep.lu.se 11 11 12 13 14 15 12 This is free software; you can redistribute it and/or modify it 13 under the terms of the GNU General Public License as published by 14 the Free Software Foundation; either version 3 of the License, or 15 (at your option) any later version. 16 16 17 18 19 20 17 The software is distributed in the hope that it will be useful, 18 but WITHOUT ANY WARRANTY; without even the implied warranty of 19 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 20 General Public License for more details. 21 21 22 23 22 You should have received a copy of the GNU General Public License 23 along with BASE. If not, see <http://www.gnu.org/licenses/>. 24 24 --> 25 25 <project name="se.lu.onk.MergeBioAssay plug-in for BASE" … … 52 52 <path id="classpath"> 53 53 <fileset dir="${basefilejar}"> 54 55 54 <include name="**/*.jar"/> 55 </fileset> 56 56 </path> 57 57 58 58 <!-- ================================= 59 59 target: compile 60 60 ================================== --> 61 61 <target name="compile" description="--> Compile the package"> … … 69 69 encoding="ISO-8859-1" 70 70 /> 71 71 </target> 72 72 73 73 <!-- ================================= 74 74 target: clean 75 75 ================================= --> 76 76 <target name="clean" description="--> Remove all generated files"> … … 83 83 84 84 <!-- ================================= 85 85 target: dist 86 86 ================================== --> 87 87 <target name="dist" depends="compile"> … … 89 89 <jar destfile="${dist}/MergeBioAssay.jar"> 90 90 <fileset dir="${build}" /> 91 92 93 94 91 <manifest> 92 <attribute name="Built-By" value="${user.name}"/> 93 <attribute name="Main-Class" value="mergebioassay.MergeBioAssay"/> 94 </manifest> 95 95 </jar> 96 96 </target> 97 97 98 98 <!-- ================================= 99 99 target: package 100 100 ================================= --> 101 101 <target name="package" depends="dist"
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