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$Id$ |
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2 |
|
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= About `se.lu.onk.Center` = |
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4 |
|
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The `se.lu.onk.Center` plug-in is a normalisation method where |
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expression values are centred around the data median or mean. See |
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``Documentation`` below for further information about the plug-in. |
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8 |
|
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`se.lu.onk.Center` is open source software. See the file `license.txt` |
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for copying conditions. |
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11 |
|
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The package was created by Johan Enell. |
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13 |
|
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14 |
|
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== Downloading == |
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16 |
|
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`se.lu.onk.Center` can be obtained from |
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18 |
|
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http://baseplugins.thep.lu.se/wiki/PluginDownload |
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20 |
|
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21 |
|
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== Installation and upgrade == |
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23 |
|
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''This plug-in is only tested in BASE through the Base1PluginExecuter |
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and may work also in BASE 1.2.17. Please report failure or success in |
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05 Nov 13 |
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BASE 1.2 through http://baseplugins.thep.lu.se. These installation |
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instructions only describe how to get the plug-in to work with the |
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Base1PluginExecuter in the latest BASE 3.x version.'' |
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29 |
|
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If you downloaded a binary package you only need to follow these |
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instructions. If you prefer to compile the package yourself, read the |
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instructions about compiling and creating a distribution before doing |
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the installation steps described here. |
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34 |
|
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You need to understand how to install plug-ins in BASE, please refer |
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to BASE documentation at http://base.thep.lu.se for general |
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instructions on plug-in installation. The BASE documentation contains |
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a chapter on plug-ins. If you have read the plug-in information you |
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should be able to follow this path |
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40 |
{{{ |
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# cd /path/to/base/plugins |
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# download Center-version.tgz |
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05 Dec 08 |
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# untar Center-version.tgz |
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05 Dec 08 |
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# ln -s Center-version Center |
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45 |
}}} |
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The symbolic link in the last line above allows for easier change to |
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future version of the plug-in. |
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48 |
{{{ |
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# Log in to your BASE as admin |
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# Upload the configuration file misc/plugin_Transformation_Center.base` |
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# Create/update a configuration for the plug-in where you select the |
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05 Dec 08 |
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plug-in definition file `plugin_Transformation_Center.base`. BASE |
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05 Dec 08 |
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will respond that plug-ins where configured but ... |
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18 Sep 08 |
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# Re-configure the plug-in without selecting a file, set the `Plugin |
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executable path` and proceed to next window by clicking |
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`Next`. This is explained in the BASE documentation and needs to |
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be done even when you update your plug-in. |
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# In this parameter window set the `Name of executable`. The value |
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of this parameter and `Plugin executables path` should add up to |
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18 Sep 08 |
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the absolute path to the binary `run`, i.e., |
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05 Dec 08 |
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/path/to/base/plugins/Center/run. How this string looks |
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like depends on your plug-in directory structure. |
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# Test the plug-ins and when you are satisfied, share it to your |
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users. |
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65 |
}}} |
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66 |
|
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67 |
|
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== Compiling == |
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69 |
|
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You must check out the `se.lu.onk.Center` from the repository and |
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follow the instructions below. Then download and untar the |
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`se.lu.onk.BaseFile` package available from |
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http://baseplugins.thep.lu.se/wiki/PluginDownload. This package is |
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16 Sep 08 |
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known to work with `se.lu.onk.BaseFile` version 1.0. |
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75 |
{{{ |
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check out project, see instructions below in section "Subversion Access" |
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# cd /path/to/se.lu.onk.Center |
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01 Oct 08 |
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# wget http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz?format=raw -O BaseFile-1.0.tgz |
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01 Oct 08 |
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# 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 |
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# optionally compare the MD5 sum of the downloaded file and the MD5-file |
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# tar zxpf BaseFile-1.0.tgz |
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# ln -s BaseFile-1.0 BaseFile |
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or |
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# mv BaseFile-1.0 BaseFile |
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85 |
}}} |
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It is important that the `BaseFile` package is located in directory |
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`BaseFile`. Now simple issue `ant`. This will create a jar file |
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`dist/Center.jar`. |
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89 |
|
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90 |
|
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== Creating a distribution == |
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92 |
|
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Update the version number in `build.xml`, and issue `ant |
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package`. This creates a distribution package with all required |
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components, including `BaseFile.jar` and associated files. |
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96 |
|
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97 |
|
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== Bug Reporting == |
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99 |
|
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You can report `se.lu.onk.Center` bugs on |
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101 |
|
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http://baseplugins.thep.lu.se/newticket |
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103 |
|
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Use user `base` and password `base`. |
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105 |
|
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106 |
|
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== Subversion Access == |
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108 |
|
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The `se.lu.onk.Center` source repository is available via anonymous |
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subversion access, issue: |
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111 |
|
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`svn co http://baseplugins.thep.lu.se/svn/plugins/base1/se.lu.onk.Center/trunk se.lu.onk.Center` |
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113 |
|
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There is no guarantees about the contents or quality of the latest |
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code in the subversion repository: it is not unheard of for code that |
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is known to be broken to be committed to the repository. Use at your |
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own risk. You may prefer to check out a released version instead, then |
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replace `trunk` with `tags/version` in the above example. |
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119 |
|
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120 |
|
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== Documentation == |
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122 |
|
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To centre your data means that data values are adjusted to reflect |
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their variation from some property of the data such as the mean or |
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05 Nov 13 |
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median. The centre plug-in allows the user to centre the expression |
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05 Dec 08 |
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levels either per gene or per array. |
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127 |
|
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05 Dec 08 |
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Consider a common experimental design where you are looking at a large |
879 |
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number of samples all compared to a common reference. For each gene, |
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05 Dec 08 |
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you have a series of ratio values that are relative to the expression |
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05 Dec 08 |
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level of that gene in the reference sample. Since the reference sample |
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05 Dec 08 |
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really has nothing to do with your experiment, you want your analysis |
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05 Dec 08 |
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to be independent of the amount of a gene present in the reference |
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sample. This is achieved by cent-er your data on genes. Centring makes |
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05 Dec 08 |
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less sense in experiments where the reference sample is part of the |
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05 Dec 08 |
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experiment. |
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137 |
|
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Centring the data for arrays can also be used to remove certain types |
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of bias and can be seen as a crude normalisation. The results of many |
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two-colour fluorescent hybridisation experiments are not corrected for |
879 |
05 Dec 08 |
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systematic biases in ratios that are the result of differences in RNA |
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amounts, labelling efficiency, and image acquisition parameters. Such |
879 |
05 Dec 08 |
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bias have the effect of multiplying ratios for all genes by a fixed |
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scalar. Mean or median centring the data in log-space has the effect |
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05 Dec 08 |
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of correcting this bias, although it should be noted that an |
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05 Dec 08 |
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assumption is being made in correcting this bias, which is that the |
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05 Dec 08 |
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average gene in a given experiment is expected to have a ratio of 1.0 |
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(or log-ratio of 0). |
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149 |
|
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In general, it is recommended that median rather than mean centring |
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is used since it is more robust against outliers. |
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152 |
|
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=== Parameters === |
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154 |
|
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''Center on genes/assays'' - Whether centring should be done on |
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05 Nov 13 |
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genes, assays, or both. If both is chosen then the centring will |
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first be done on genes then on assays, this is called a cycle. |
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158 |
|
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''Assay groups for centering'' - If the centring should be based on |
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05 Nov 13 |
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data in one or more assay groups. If `Default` is selected, centring |
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05 Nov 13 |
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on assays is made with each assay in its own group, while centring on |
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05 Nov 13 |
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genes is made with all assays in one group. Selecting `Single assay |
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05 Nov 13 |
jari |
group` centres all data based on values in a single assay |
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05 Nov 13 |
jari |
group. `Assay groups` centres each assay group separately. |
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165 |
|
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''Center group(s) assay names'' - Comma-separated list of names of |
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05 Nov 13 |
jari |
assays in groups to use for centring, with each group separated by a |
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05 Nov 13 |
jari |
`|` character. This option is only used when `Single assay group` or |
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05 Nov 13 |
jari |
`Assay groups` has been selected under ''Assay groups for centering''. |
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170 |
|
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05 Dec 08 |
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''Number of centering cycles'' - How many cycles should be done during |
879 |
05 Dec 08 |
jari |
centering. This value is only relevant if the centering should be done |
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on both genes and assays. |
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174 |
|
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05 Dec 08 |
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''Centering using median or mean'' - Whether median or mean should be |
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05 Dec 08 |
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used for the centering. |
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177 |
|
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''Normalise on gene/assays using median or mean'' - Whether |
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05 Nov 13 |
jari |
normalisation should be done on genes, assays, or both. |
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18 Sep 08 |
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180 |
|
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05 Nov 13 |
jari |
''Number of normalization cycles'' - How many cycles should be done |
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05 Nov 13 |
jari |
during normalisation. |
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05 Nov 13 |
jari |
183 |
|
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05 Nov 13 |
jari |
''Create debug files'' - If debug data should be stored in `data` |
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05 Nov 13 |
jari |
directory. |
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05 Nov 13 |
jari |
186 |
|
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187 |
---------------------------------------------------------------------- |
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188 |
{{{ |
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05 Nov 13 |
jari |
Copyright (C) 2008, 2013 Jari Häkkinen |
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190 |
|
875 |
05 Dec 08 |
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This file is part of the se.lu.onk.Center plug-in for BASE. Available |
875 |
05 Dec 08 |
jari |
at http://baseplugins.thep.lu.se/ and BASE web site is |
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16 Sep 08 |
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http://base.thep.lu.se |
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16 Sep 08 |
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194 |
|
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This is free software; you can redistribute it and/or modify it under |
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16 Sep 08 |
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the terms of the GNU General Public License as published by the Free |
766 |
16 Sep 08 |
jari |
Software Foundation; either version 3 of the License, or (at your |
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16 Sep 08 |
jari |
option) any later version. |
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199 |
|
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This package is distributed in the hope that it will be useful, but |
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16 Sep 08 |
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WITHOUT ANY WARRANTY; without even the implied warranty of |
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16 Sep 08 |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 Sep 08 |
jari |
General Public License for more details. |
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16 Sep 08 |
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204 |
|
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You should have received a copy of the GNU General Public License |
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16 Sep 08 |
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along with this package. If not, see <http://www.gnu.org/licenses/>. |
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207 |
}}} |