Changeset 895


Ignore:
Timestamp:
Dec 8, 2008, 10:39:49 AM (13 years ago)
Author:
Jari Häkkinen
Message:

Addresses #56 and #159. Creating VirtualArray? module.

Location:
plugins/base1
Files:
2 added
3 edited
3 copied
1 moved

Legend:

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

    r893 r895  
    11$Id$
    22
    3 = About `se.lu.onk.Center` =
     3= About `se.lu.onk.VirtualArray` =
    44
    5 The `se.lu.onk.Center` plug-in is a normalisation method where
    6 expression values are centered around the data median or mean. See
    7 ``Documentation`` below for further information about the plug-in.
     5The `se.lu.onk.VirtualArray` plug-in is a ...
    86
    9 `se.lu.onk.Center` is free software. See the file license.txt for
    10 copying conditions.
     7`se.lu.onk.VirtualArray` is free software. See the file license.txt
     8for copying conditions.
    119
    1210The package was created by Johan Enell and is currently maintained by
     
    1614== Downloading ==
    1715
    18 `se.lu.onk.Center` can be obtained from
     16`se.lu.onk.VirtualArray` can be obtained from
    1917
    2018  http://baseplugins.thep.lu.se/wiki/PluginDownload
     
    4240{{{
    4341  # cd /path/to/base/plugins
    44   # download Center-version.tgz
    45   # untar Center-version.tgz
    46   # ln -s Center-version Center
     42  # download VirtualArray-version.tgz
     43  # untar VirtualArray-version.tgz
     44  # ln -s VirtualArray-version VirtualArray
    4745}}}
    4846The symbolic link in the last line above allows for easier change to
     
    5048{{{
    5149  # Log in to your BASE as admin
    52   # Upload the configuration file misc/plugin_Transformation_Center.base`
     50  # Upload the configuration file lib/pluginVirtualArray.base`
    5351  # Create/update a configuration for the plug-in where you select the
    54     plug-in definition file `plugin_Transformation_Center.base`. BASE
     52    plug-in definition file `pluginVirtualArray.base`. BASE
    5553    will respond that plug-ins where configured but ...
    5654  # Re-configure the plug-in without selecting a file, set the `Plugin
     
    6159    of this parameter and `Plugin executables path` should add up to
    6260    the absolute path to the binary `run`, i.e.,
    63     /path/to/base/plugins/Center/run. How this string looks
     61    /path/to/base/plugins/VirtualArray/run. How this string looks
    6462    like depends on your plug-in directory structure.
    6563  # Test the plug-ins and when you are satisfied, share it to your
     
    7068== Compiling ==
    7169
    72 You must checkout the `se.lu.onk.Center` from the repository,
     70You must checkout the `se.lu.onk.VirtualArray` from the repository,
    7371follow the instructions below. Then download and untar the
    7472`se.lu.onk.BaseFile` package available from
     
    7775{{{
    7876  check out project, see instructions below
    79   # cd /path/to/se.lu.onk.Center
     77  # cd /path/to/se.lu.onk.VirtualArray
    8078  # wget http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz?format=raw -O BaseFile-1.0.tgz
    8179  # wget http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz.MD5?format=raw -O BaseFile-1.0.tgz.MD5
     
    8886It is important that the `BaseFile` package is located in directory
    8987`BaseFile`. Now simple issue `ant`. This will create a jar file
    90 `dist/Center.jar`.
     88`dist/VirtualArray.jar`.
    9189
    9290
     
    10098== Bug Reporting ==
    10199
    102 You can report `se.lu.onk.Center` bugs on
     100You can report `se.lu.onk.VirtualArray` bugs on
    103101
    104102  http://baseplugins.thep.lu.se/newticket
     
    109107== Subversion Access ==
    110108
    111 The `se.lu.onk.Center` source repository is available via anonymous
     109The `se.lu.onk.VirtualArray` source repository is available via anonymous
    112110subversion access, issue:
    113111
    114   `svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.Center/trunk se.lu.onk.Center`
     112  `svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.VirtualArray/trunk se.lu.onk.VirtualArray`
    115113
    116114There is no guarantees about the contents or quality of the latest
     
    121119
    122120
    123 == Documentation ==
    124 
    125 To center your data means that data values are adjusted to reflect
    126 their variation from some property of the data such as the mean or
    127 median. The center plug-in allows the user to center the expression
    128 levels either per gene or per array.
    129 
    130 Consider a common experimental design where you are looking at a large
    131 number of samples all compared to a common reference. For each gene,
    132 you have a series of ratio values that are relative to the expression
    133 level of that gene in the reference sample. Since the reference sample
    134 really has nothing to do with your experiment, you want your analysis
    135 to be independent of the amount of a gene present in the reference
    136 sample. This is achieved by center your data on genes. Centering makes
    137 less sense in experiments where the reference sample is part of the
    138 experiment.
    139 
    140 Centering the data for arrays can also be used to remove certain types
    141 of bias and can be seen as a crude normalization. The results of many
    142 two-color fluorescent hybridization experiments are not corrected for
    143 systematic biases in ratios that are the result of differences in RNA
    144 amounts, labeling efficiency, and image acquisition parameters. Such
    145 bias have the effect of multiplying ratios for all genes by a fixed
    146 scalar. Mean or median centering the data in log-space has the effect
    147 of correcting this bias, although it should be noted that an
    148 assumption is being made in correcting this bias, which is that the
    149 average gene in a given experiment is expected to have a ratio of 1.0
    150 (or log-ratio of 0).
    151 
    152 In general, it is recommended that median rather than mean centering
    153 is used since it is more robust against outliers.
    154 
    155 === Parameters ===
    156 
    157 ''Center on genes/arrays'' - Whether centering should be done on
    158 genes, arrays or both. If both is chosen then the centering will first
    159 be done on genes then on arrays, this is called a cycle.
    160 
    161 ''Number of centering cycles'' - How many cycles should be done during
    162 centering. This value is only relevant if the centering should be done
    163 on both genes and arrays.
    164 
    165 ''Centering using median or mean'' - Whether median or mean should be
    166 used for the centering.
    167 
    168 
    169121----------------------------------------------------------------------
    170122{{{
    171123Copyright (C) 2008 Jari Häkkinen
    172124
    173 This file is part of the se.lu.onk.Center plug-in for BASE. Available
    174 at http://baseplugins.thep.lu.se/ and BASE web site is
     125This file is part of the se.lu.onk.VirtualArray plug-in for
     126BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site is
    175127http://base.thep.lu.se
    176128
  • plugins/base1/se.lu.onk.VirtualArray/trunk/build.xml

    r893 r895  
    2323    along with this software. If not, see <http://www.gnu.org/licenses/>.
    2424-->
    25 <project name="se.lu.onk.Center plug-in for BASE"
     25<project name="se.lu.onk.VirtualArray plug-in for BASE"
    2626         default="dist" basedir=".">
    2727  <description>
    28     This build file is used for se.lu.onk.Center plug-in for
     28    This build file is used for se.lu.onk.VirtualArray plug-in for
    2929    BASE created at the Department of Oncology, Lund University,
    3030    Sweden.
     
    4040       1.0, 1.1, 1.2pre
    4141    -->
    42   <property name="version" value="2.2pre" />
     42  <property name="version" value="1.1pre" />
    4343
    4444  <property name="basefilejar" value="BaseFile" />
    4545  <property name="build" location="build" />
    4646  <property name="dist" location="dist" />
    47   <property name="misc" location="misc" />
     47  <property name="lib" location="lib" />
    4848  <property name="package" value="mergebioassay"/>
    49   <property name="packagestring" value="Center-${version}" />
     49  <property name="packagestring" value="VirtualArray-${version}" />
    5050  <property name="src" location="src" />
    5151 
     
    8787  <target name="dist" depends="compile">
    8888    <mkdir dir="${dist}" />
    89     <jar destfile="${dist}/Center.jar">
     89    <jar destfile="${dist}/VirtualArray.jar">
    9090      <fileset dir="${build}" />
    9191      <manifest>
     
    104104    <mkdir dir="${package}/${basefilejar}"/>
    105105    <copy todir="${package}">
    106       <fileset file="${dist}/Center.jar" />
    107       <fileset dir="${misc}" />
     106      <fileset file="${dist}/VirtualArray.jar" />
     107      <fileset dir="${lib}" />
    108108      <fileset file="license.txt" />
    109109      <fileset file="README" />
  • plugins/base1/se.lu.onk.VirtualArray/trunk/lib/run

    r149 r895  
    11#!/bin/bash -
     2#
     3# $Id: run 880 2008-12-05 11:28:29Z jari $
     4#
     5# Copyright (C) 2004 Johan Enell
     6# Copyright (C) 2008 Jari Häkkinen
     7#
     8# This file is part of the se.lu.onk.Center plug-in for
     9# BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site
     10# is http://base.thep.lu.se
     11#
     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#
     17# The software is distributed in the hope that it will be useful, but
     18# 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#
     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#
    225
    326progdir="`dirname \"$0\"`"
    4 java -cp "$CLASSPATH:$progdir/VirtualArray.jar" virtualarray.VirtualArray
     27java -cp "$CLASSPATH:$progdir/BaseFile/BaseFile.jar:$progdir/VirtualArray.jar" virtualarray.VirtualArray
  • plugins/base1/se.lu.onk.VirtualArray/trunk/src/virtualarray/VirtualArray.java

    • Property svn:keywords set to Id
    r270 r895  
     1/*
     2 * $Id$
     3 *
     4 * Copyright (C) 2004 Johan Enell
     5 * Copyright (C) 2008 Jari Häkkinen
     6 *
     7 * This file is part of the se.lu.onk.Center plug-in for
     8 * BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site
     9 * is http://base.thep.lu.se
     10 *
     11 * This is free software; you can redistribute it and/or modify it
     12 * under the terms of the GNU General Public License as published by
     13 * the Free Software Foundation; either version 3 of the License, or
     14 * (at your option) any later version.
     15 *
     16 * The software is distributed in the hope that it will be useful, but
     17 * WITHOUT ANY WARRANTY; without even the implied warranty of
     18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
     19 * General Public License for more details.
     20 *
     21 * You should have received a copy of the GNU General Public License
     22 * along with this software. If not, see <http://www.gnu.org/licenses/>.
     23 */
     24
    125package virtualarray;
    2 /*
    3  * Created on 05-Nov-2004
    4  *
    5  * VirtualArray.java is a part of QPackage
    6  * Copyright (C) 2004 Johan Enell, Dept Oncology, Lund University
    7  *
    8  * This program is free software; you can redistribute it and/or
    9  * modify it under the terms of the GNU General Public License
    10  * as published by the Free Software Foundation; either version 2
    11  * of the License, or (at your option) any later version.
    12  *
    13  * This program is distributed in the hope that it will be useful,
    14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
    15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    16  * GNU General Public License for more details.
    17  *
    18  * You should have received a copy of the GNU General Public License
    19  * along with this program; if not, write toX the Free Software
    20  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
    21  */
    2226
    2327import java.io.File;
  • plugins/base1/se.lu.onk/trunk/build.xml

    r875 r895  
    1616  <!-- lib -->
    1717  <property name="lib" location="lib" />
    18   <property name="virtualarray.lib" location="VirtualArray/lib" />
    1918  <property name="qpackage.lib" location="QPackage/lib" />
    2019  <property name="smooth.doc" location="smooth/doc" />
     
    2221  <!-- src -->
    2322  <property name="basefile.src" location="BaseFile/src" />
    24   <property name="virtualarray.src" location="VirtualArray/src" />
    2523  <property name="qpackage.src" location="QPackage/src" />
    2624  <property name="normalization.src" location="Normalization/src" />
     
    3432  <property name="bin" location="build" />
    3533  <property name="basefile.bin" location="${bin}/BaseFile" />
    36   <property name="virtualarray.bin" location="${bin}/VirtualArray" />
    3734  <property name="qpackage.bin" location="${bin}/QPackage" />
    3835  <property name="normalization.bin" location="${bin}/Normalization" />
     
    6158    ================================== -->
    6259  <target name="compile" description="--> Compiles all the packages">
    63     <ant target="virtualarray.compile" />
    6460    <ant target="qpackage.compile" />
    6561    <ant target="normalization.compile" />
     
    8278
    8379  <!-- - - - - - - - - - - - - - - - - -
    84       target: virtualarray.compile
    85      - - - - - - - - - - - - - - - - - -->
    86     <target name="virtualarray.compile" depends="basefile.compile">
    87       <mkdir dir="${virtualarray.bin}"/>
    88       <javac
    89         srcdir="${virtualarray.src}"
    90         destdir="${virtualarray.bin}"
    91         classpath="${basefile.bin}"
    92         debug="true"
    93         deprecation="true"
    94         encoding="ISO-8859-1"
    95       />
    96     </target>
    97  
    98   <!-- - - - - - - - - - - - - - - - - -
    9980      target: qpackage.compile
    10081     - - - - - - - - - - - - - - - - - -->
     
    216197    ================================== -->
    217198  <target name="dist"
    218     depends="virtualarray.dist,
    219       qpackage.dist, lowess.dist, smooth.dist"
     199    depends="qpackage.dist, lowess.dist, smooth.dist"
    220200    description="--> Creates a ditributable gzipfile for each package">
    221   </target>
    222  
    223   <!-- - - - - - - - - - - - - - - - - -
    224       target: virtualarray.dist                     
    225      - - - - - - - - - - - - - - - - - -->
    226   <target name="virtualarray.dist" depends="virtualarray.compile">
    227     <mkdir dir="${dist}" />
    228     <jar destfile="${dist}/virtualarray.jar">
    229       <fileset dir="${basefile.src}" />
    230       <fileset dir="${basefile.bin}" />
    231       <fileset dir="${virtualarray.bin}" />
    232       <fileset dir="${virtualarray.src}" />
    233         <manifest>
    234           <attribute name="Built-By" value="${user.name}" />
    235           <attribute name="Main-Class" value="virtualarray.VirtualArray" />
    236         </manifest>
    237     </jar>
    238201  </target>
    239202 
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