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plugins/base1/se.lu.onk.Center/trunk/README
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$Id: README 879 2008-12-05 10:28:12Z jari $
About se.lu.onk.Center
The se.lu.onk.Center plug-in is a normalisation method where
expression values are centered around the data median or mean. See
Documentation below for further information about the plug-in.
se.lu.onk.Center is free software. See the file license.txt for
copying conditions.
The package was created by Johan Enell and is currently maintained by Jari Häkkinen.
Downloading
se.lu.onk.Center can be obtained from
Installation and upgrade
This plug-in is only tested in BASE 2.8 through the Base1PluginExecuter but is expected to 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 version 2.
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
executables 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 checkout the se.lu.onk.Center from the repository,
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
# 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
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 center 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 center plug-in allows the user to center 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 center your data on genes. Centering makes less sense in experiments where the reference sample is part of the experiment.
Centering the data for arrays can also be used to remove certain types of bias and can be seen as a crude normalization. The results of many two-color fluorescent hybridization experiments are not corrected for systematic biases in ratios that are the result of differences in RNA amounts, labeling efficiency, and image acquisition parameters. Such bias have the effect of multiplying ratios for all genes by a fixed scalar. Mean or median centering 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 centering is used since it is more robust against outliers.
Parameters
Center on genes/arrays - Whether centering should be done on genes, arrays or both. If both is chosen then the centering will first be done on genes then on arrays, this is called a cycle.
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 arrays.
Centering using median or mean - Whether median or mean should be used for the centering.
Copyright (C) 2008 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 <http://www.gnu.org/licenses/>.
