$Id: README 2118 2013-11-05 14:44:53Z jari $ = About `se.lu.onk.Center` = The `se.lu.onk.Center` plug-in is a normalisation method where expression values are centred around the data median or mean. See ``Documentation`` below for further information about the plug-in. `se.lu.onk.Center` is open source software. See the file `license.txt` for copying conditions. The package was created by Johan Enell. == Downloading == `se.lu.onk.Center` can be obtained from http://baseplugins.thep.lu.se/wiki/PluginDownload == Installation and upgrade == ''This plug-in is only tested in BASE through the Base1PluginExecuter and may work also in BASE 1.2.17. Please report failure or success in BASE 1.2 through http://baseplugins.thep.lu.se. These installation instructions only describe how to get the plug-in to work with the Base1PluginExecuter in the latest BASE 3.x version.'' If you downloaded a binary package you only need to follow these instructions. If you prefer to compile the package yourself, read the instructions about compiling and creating a distribution before doing the installation steps described here. You need to understand how to install plug-ins in BASE, please refer to BASE documentation at http://base.thep.lu.se for general instructions on plug-in installation. The BASE documentation contains a chapter on plug-ins. If you have read the plug-in information you should be able to follow this path {{{ # cd /path/to/base/plugins # download Center-version.tgz # untar Center-version.tgz # ln -s Center-version Center }}} The symbolic link in the last line above allows for easier change to future version of the plug-in. {{{ # Log in to your BASE as admin # Upload the configuration file misc/plugin_Transformation_Center.base` # Create/update a configuration for the plug-in where you select the plug-in definition file `plugin_Transformation_Center.base`. BASE will respond that plug-ins where configured but ... # Re-configure the plug-in without selecting a file, set the `Plugin executable path` and proceed to next window by clicking `Next`. This is explained in the BASE documentation and needs to be done even when you update your plug-in. # In this parameter window set the `Name of executable`. The value of this parameter and `Plugin executables path` should add up to the absolute path to the binary `run`, i.e., /path/to/base/plugins/Center/run. How this string looks like depends on your plug-in directory structure. # Test the plug-ins and when you are satisfied, share it to your users. }}} == Compiling == You must check out the `se.lu.onk.Center` from the repository and follow the instructions below. Then download and untar the `se.lu.onk.BaseFile` package available from http://baseplugins.thep.lu.se/wiki/PluginDownload. This package is known to work with `se.lu.onk.BaseFile` version 1.0. {{{ check out project, see instructions below in section "Subversion Access" # cd /path/to/se.lu.onk.Center # wget http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz?format=raw -O BaseFile-1.0.tgz # 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 # optionally compare the MD5 sum of the downloaded file and the MD5-file # tar zxpf BaseFile-1.0.tgz # ln -s BaseFile-1.0 BaseFile or # mv BaseFile-1.0 BaseFile }}} It is important that the `BaseFile` package is located in directory `BaseFile`. Now simple issue `ant`. This will create a jar file `dist/Center.jar`. == Creating a distribution == Update the version number in `build.xml`, and issue `ant package`. This creates a distribution package with all required components, including `BaseFile.jar` and associated files. == Bug Reporting == You can report `se.lu.onk.Center` bugs on http://baseplugins.thep.lu.se/newticket Use user `base` and password `base`. == Subversion Access == The `se.lu.onk.Center` source repository is available via anonymous subversion access, issue: `svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.Center/trunk se.lu.onk.Center` There is no guarantees about the contents or quality of the latest code in the subversion repository: it is not unheard of for code that is known to be broken to be committed to the repository. Use at your own risk. You may prefer to check out a released version instead, then replace `trunk` with `tags/version` in the above example. == Documentation == To centre your data means that data values are adjusted to reflect their variation from some property of the data such as the mean or median. The centre plug-in allows the user to centre the expression levels either per gene or per array. Consider a common experimental design where you are looking at a large number of samples all compared to a common reference. For each gene, you have a series of ratio values that are relative to the expression level of that gene in the reference sample. Since the reference sample really has nothing to do with your experiment, you want your analysis to be independent of the amount of a gene present in the reference sample. This is achieved by cent-er your data on genes. Centring makes less sense in experiments where the reference sample is part of the experiment. Centring the data for arrays can also be used to remove certain types of bias and can be seen as a crude normalisation. The results of many two-colour fluorescent hybridisation experiments are not corrected for systematic biases in ratios that are the result of differences in RNA amounts, labelling efficiency, and image acquisition parameters. Such bias have the effect of multiplying ratios for all genes by a fixed scalar. Mean or median centring the data in log-space has the effect of correcting this bias, although it should be noted that an assumption is being made in correcting this bias, which is that the average gene in a given experiment is expected to have a ratio of 1.0 (or log-ratio of 0). In general, it is recommended that median rather than mean centring is used since it is more robust against outliers. === Parameters === ''Center on genes/assays'' - Whether centring should be done on genes, assays, or both. If both is chosen then the centring will first be done on genes then on assays, this is called a cycle. ''Assay groups for centering'' - If the centring should be based on data in one or more assay groups. If `Default` is selected, centring on assays is made with each assay in its own group, while centring on genes is made with all assays in one group. Selecting `Single assay group` centres all data based on values in a single assay group. `Assay groups` centres each assay group separately. ''Center group(s) assay names'' - Comma-separated list of names of assays in groups to use for centring, with each group separated by a `|` character. This option is only used when `Single assay group` or `Assay groups` has been selected under ''Assay groups for centering''. ''Number of centering cycles'' - How many cycles should be done during centering. This value is only relevant if the centering should be done on both genes and assays. ''Centering using median or mean'' - Whether median or mean should be used for the centering. ''Normalise on gene/assays using median or mean'' - Whether normalisation should be done on genes, assays, or both. ''Number of normalization cycles'' - How many cycles should be done during normalisation. ''Create debug files'' - If debug data should be stored in `data` directory. ---------------------------------------------------------------------- {{{ Copyright (C) 2008, 2013 Jari Häkkinen This file is part of the se.lu.onk.Center plug-in for BASE. Available at http://baseplugins.thep.lu.se/ and BASE web site is http://base.thep.lu.se This is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this package. If not, see . }}}