$Id: README 804 2008-10-01 14:44:29Z jari $

About se.lu.onk.MergeBioAssay

The se.lu.onk.MergeBioAssay plug-in merge bioassays by grouping them according to annotation types or syntactical differences in the name. See Documentation below fo further information about the plug-in.

se.lu.onk.MergeBioAssay 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.MergeBioAssay can be obtained from

​http://baseplugins.thep.lu.se/wiki/PluginDownload

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 MergeBioAssay-version.tgz
  # untar MergeBioAssay-version.tgz
  # ln -s MergeBioAssay-version MergeBioAssay

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 `mergebioassay.base`
  # Create/update a configuration for the plug-in where you select the
    plug-in defintion files `mergebioassay.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/MergeBioAssay/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.MergeBioAssay 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.MergeBioAssay
  # 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/MergeBioAssay.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.MergeBioAssay bugs on

​http://baseplugins.thep.lu.se/newticket

Use user base and password base.

Subversion Access

The se.lu.onk.MergeBioAssay source repository is available via anonymous subversion access, issue:

svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.MergeBioAssay/trunk se.lu.onk.MergeBioAssay

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

This plug-in base-users merge bioassays by grouping them according to annotation types or syntactical differences in the name. There are four different methods for calculating the merged values. They differ in what kind of mean they are using (arithmetic or geometric) and if they are merging on ratio or intensity.

For each group the parents are saved so the link to the raw data is preserved. Annotations for the bioassays are saved if sample1 is the same for each assay in each group.

Merge methods

Geometric mean of ratio::

This method calculates the geometric mean of the ratios in each group per position.

Arithmetic mean of ratio::

This method calculates the arithmetic mean of the ratios in each group per position.

Arithmetic mean of intensity::

This method calculates the arithmetic mean of the intensities in each group per position.

Ratio of ratio::

This method works a little bit different from the others. It requires that each group consists of exactly two bioassays. It will then create a new ratio for each spot with one of the assays over the other, depending on what the user has specified in the ratio parameters.

Parameters

Assayname::

This parameter specifies how the name of the assays is constructed. Use %0-%9 as wildcards and then put any character(s) between as delimiters. For example assay name Assay_1_A can be divided into three parts. By setting the parameter to %1_%2_%3 the plugin will read assay name assay_1_A and set %1=Assay, %2=1 and %3=A. Thus, if your assays have names constructed in the same way merge can sort the assays in groups depending on %1, %2 or %3.

Group::

This will specify how the assays will be grouped together. It can either be a %-number used in assayname or an annotation type.

Example 1: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be sorted into groups of assays using merge.

A: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222 = %2 will sort the assays into two groups.

One group were %2=1  (assays Assay_1_A and Assay_1_B)
One group were %2=2  (assays Assay_2_A and Assay_2_B)

B: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222 = %3 will sort the assays into two groups.

One group were %3=A  (assays Assay_1_A and Assay_2_A)
One group were %3=B  (assays Assay_1_B and Assay_1_B)

New name::

This text will be used in the name of the merged assays. The name will be this string followed by the groupname.

Merge method::

Choose one of the methodes described above.

Ratio::

If merge method ratio of ratio is chosen the form of the ratio must be specified. This is done either in the ratio parameter or in ratio annotation type and ratio annotation value. In the ratio parameter you can choose a %-number followed by the two values it can take. The last character in the string must be the delimiter the user has choosen ot use. The other way a user can specify the ratio is by choosing an annotation type in the list and specify the values in the annotation values parameter. This is done by writing the values with the delimiter used last,

%1|vr1|vr2|

This will take the values from %1 in the assayname and put the assay with value vr1 over the assay with values vr2. Notice that the final character is the delimiter (this can of course be any character).

Example 2: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be sorted into groups of assays using merge.

A: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter \221Group\222 = %2 will sort the assays into two groups.

One group were %2=1  (assays Assay_1_A and Assay_1_B)
One group were %2=2  (assays Assay_2_A and Assay_2_B)

B: By setting parameter \221Ratio\222 = %3|A|B| ratios of ratios will be created as:

Assay_1_A / Assay_1_B
Assay_2_A / Assay_2_B

References

​Arithmetic mean
​Geometric mean

---

Copyright (C) 2008 Jari Häkkinen
This file is part of the se.lu.onk.MergeBioAssay 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/>.