Changeset 788


Ignore:
Timestamp:
Sep 18, 2008, 11:02:25 PM (14 years ago)
Author:
Jari Häkkinen
Message:

Addresses #137. Added documentation.

Location:
plugins/base1/se.lu.onk.MergeBioAssay/trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • plugins/base1/se.lu.onk.MergeBioAssay/trunk/README

    r776 r788  
    33= About `se.lu.onk.MergeBioAssay` =
    44
    5 The `se.lu.onk.MergeBioAssay` plug-in for BASE is
     5The `se.lu.onk.MergeBioAssay` plug-in merge bioassays by grouping them
     6according to annotation types or syntactical differences in the
     7name. See ``Documentation`` below fo further information about the
     8plug-in.
    69
    710`se.lu.onk.MergeBioAssay` is free software. See the file license.txt for
     
    7881  # wget http://baseplugins.thep.lu.se/.../BaseFile-1.0.tgz
    7982  # wget http://baseplugins.thep.lu.se/.../BaseFile-1.0.tgz.MD5
    80   # optionally compare the MD5 sum of the downloaded file and the MD5-file
     83  # optionally compare the MD5 sum of the downloaded file and the MD5-file
    8184  # tar zxpf BaseFile-1.0.tgz
    8285  # ln -s BaseFile-1.0 BaseFile
     
    98101== Bug Reporting ==
    99102
    100 You can report `se.lu.onk.MergeBioAssay` bugs on 
     103You can report `se.lu.onk.MergeBioAssay` bugs on
    101104
    102105  http://baseplugins.thep.lu.se/newticket
     
    119122
    120123
     124== Documentation ==
     125
     126This plug-in base-users merge bioassays by grouping them according to
     127annotation types or syntactical differences in the name. There are
     128four different methods for calculating the merged values. They differ
     129in what kind of mean they are using (arithmetic or geometric) and if
     130they are merging on ratio or intensity.
     131
     132For each group the parents are saved so the link to the raw data is
     133preserved. Annotations for the bioassays are saved if sample1 is the
     134same 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{{{
     178One group were %2=1  (assays Assay_1_A and Assay_1_B)
     179One 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{{{
     184One group were %3=A  (assays Assay_1_A and Assay_2_A)
     185One 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{{{
     218One group were %2=1  (assays Assay_1_A and Assay_1_B)
     219One 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{{{
     224Assay_1_A / Assay_1_B
     225Assay_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
    121233
    122234----------------------------------------------------------------------
  • plugins/base1/se.lu.onk.MergeBioAssay/trunk/build.xml

    r783 r788  
    11<?xml version="1.0" encoding="UTF-8"?>
    22<!--
    3     $Id$
     3    $Id$
    44
    5     Copyright (C) 2005, 2006 Johan Enell
    6     Copyright (C) 2008 Jari Häkkinen
     5    Copyright (C) 2005, 2006 Johan Enell
     6    Copyright (C) 2008 Jari Häkkinen
    77
    8     This file is part of the se.lu.onk.MergeBioAssay plug-in for
     8    This file is part of the se.lu.onk.MergeBioAssay plug-in for
    99    BASE. Available at http://baseplugins.thep.lu.se/ and BASE web
    1010    site is http://base.thep.lu.se
    1111
    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.
     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.
    1616
    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.
     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.
    2121
    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/>.
     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/>.
    2424-->
    2525<project name="se.lu.onk.MergeBioAssay plug-in for BASE"
     
    5252  <path id="classpath">
    5353    <fileset dir="${basefilejar}">
    54       <include name="**/*.jar"/>
    55     </fileset>
     54      <include name="**/*.jar"/>
     55    </fileset>
    5656  </path>
    5757 
    5858  <!-- =================================
    59       target: compile
     59      target: compile
    6060    ================================== -->
    6161  <target name="compile" description="--> Compile the package">
     
    6969       encoding="ISO-8859-1"
    7070       />
    71   </target>
     71  </target>
    7272 
    7373  <!-- =================================
    74       target: clean
     74      target: clean
    7575     ================================= -->
    7676  <target name="clean" description="--> Remove all generated files">
     
    8383
    8484  <!-- =================================
    85       target: dist
     85      target: dist
    8686    ================================== -->
    8787  <target name="dist" depends="compile">
     
    8989    <jar destfile="${dist}/MergeBioAssay.jar">
    9090      <fileset dir="${build}" />
    91       <manifest>
    92         <attribute name="Built-By" value="${user.name}"/>
    93         <attribute name="Main-Class" value="mergebioassay.MergeBioAssay"/>
    94       </manifest>
     91      <manifest>
     92        <attribute name="Built-By" value="${user.name}"/>
     93        <attribute name="Main-Class" value="mergebioassay.MergeBioAssay"/>
     94      </manifest>
    9595    </jar>
    9696  </target>
    9797 
    9898  <!-- =================================
    99       target: package
     99      target: package
    100100     ================================= -->
    101101  <target name="package" depends="dist"
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