Changeset 2118


Ignore:
Timestamp:
Nov 5, 2013, 3:44:53 PM (8 years ago)
Author:
Jari Häkkinen
Message:

Addresses #79. Updated README to reflect changes made in ticket:79

File:
1 edited

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  • plugins/base1/se.lu.onk.Center/trunk/README

    r879 r2118  
    44
    55The `se.lu.onk.Center` plug-in is a normalisation method where
    6 expression values are centered around the data median or mean. See
     6expression values are centred around the data median or mean. See
    77``Documentation`` below for further information about the plug-in.
    88
    9 `se.lu.onk.Center` is free software. See the file license.txt for
    10 copying conditions.
    11 
    12 The package was created by Johan Enell and is currently maintained by
    13 Jari Häkkinen.
     9`se.lu.onk.Center` is open source software. See the file `license.txt`
     10for copying conditions.
     11
     12The package was created by Johan Enell.
    1413
    1514
     
    2322== Installation and upgrade ==
    2423
    25 ''This plug-in is only tested in BASE 2.8 through the
    26 Base1PluginExecuter but is expected to work also in BASE
    27 1.2.17. Please report failure or success in BASE 1.2 through
    28 http://baseplugins.thep.lu.se. These installation instructions only
    29 describe how to get the plug-in to work with the Base1PluginExecuter
    30 in the latest BASE version 2.''
     24''This plug-in is only tested in BASE through the Base1PluginExecuter
     25and may work also in BASE 1.2.17. Please report failure or success in
     26BASE 1.2 through http://baseplugins.thep.lu.se. These installation
     27instructions only describe how to get the plug-in to work with the
     28Base1PluginExecuter in the latest BASE 3.x version.''
    3129
    3230If you downloaded a binary package you only need to follow these
     
    5553    will respond that plug-ins where configured but ...
    5654  # Re-configure the plug-in without selecting a file, set the `Plugin
    57     executables path` and proceed to next window by clicking
     55    executable path` and proceed to next window by clicking
    5856    `Next`. This is explained in the BASE documentation and needs to
    5957    be done even when you update your plug-in.
     
    7068== Compiling ==
    7169
    72 You must checkout the `se.lu.onk.Center` from the repository,
     70You must check out the `se.lu.onk.Center` from the repository and
    7371follow the instructions below. Then download and untar the
    7472`se.lu.onk.BaseFile` package available from
     
    7674known to work with `se.lu.onk.BaseFile` version 1.0.
    7775{{{
    78   check out project, see instructions below
     76  check out project, see instructions below in section "Subversion Access"
    7977  # cd /path/to/se.lu.onk.Center
    8078  # wget http://baseplugins.thep.lu.se/attachment/wiki/se.lu.onk.BaseFile/BaseFile-1.0.tgz?format=raw -O BaseFile-1.0.tgz
     
    9593Update the version number in `build.xml`, and issue `ant
    9694package`. This creates a distribution package with all required
    97 components, including BaseFile.jar and associated files.
     95components, including `BaseFile.jar` and associated files.
    9896
    9997
     
    123121== Documentation ==
    124122
    125 To center your data means that data values are adjusted to reflect
     123To centre your data means that data values are adjusted to reflect
    126124their 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
     125median. The centre plug-in allows the user to centre the expression
    128126levels either per gene or per array.
    129127
     
    134132really has nothing to do with your experiment, you want your analysis
    135133to 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
     134sample. This is achieved by cent-er your data on genes. Centring makes
    137135less sense in experiments where the reference sample is part of the
    138136experiment.
    139137
    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
     138Centring the data for arrays can also be used to remove certain types
     139of bias and can be seen as a crude normalisation. The results of many
     140two-colour fluorescent hybridisation experiments are not corrected for
    143141systematic biases in ratios that are the result of differences in RNA
    144 amounts, labeling efficiency, and image acquisition parameters. Such
     142amounts, labelling efficiency, and image acquisition parameters. Such
    145143bias 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
     144scalar. Mean or median centring the data in log-space has the effect
    147145of correcting this bias, although it should be noted that an
    148146assumption is being made in correcting this bias, which is that the
     
    150148(or log-ratio of 0).
    151149
    152 In general, it is recommended that median rather than mean centering
     150In general, it is recommended that median rather than mean centring
    153151is used since it is more robust against outliers.
    154152
    155153=== Parameters ===
    156154
    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.
     155''Center on genes/assays'' - Whether centring should be done on
     156genes, assays, or both. If both is chosen then the centring will
     157first be done on genes then on assays, this is called a cycle.
     158
     159''Assay groups for centering'' - If the centring should be based on
     160data in one or more assay groups. If `Default` is selected, centring
     161on assays is made with each assay in its own group, while centring on
     162genes is made with all assays in one group. Selecting `Single assay
     163group` centres all data based on values in a single assay
     164group. `Assay groups` centres each assay group separately.
     165
     166''Center group(s) assay names'' - Comma-separated list of names of
     167assays in groups to use for centring, with each group separated by a
     168`|` character. This option is only used when `Single assay group` or
     169`Assay groups` has been selected under ''Assay groups for centering''.
    160170
    161171''Number of centering cycles'' - How many cycles should be done during
    162172centering. This value is only relevant if the centering should be done
    163 on both genes and arrays.
     173on both genes and assays.
    164174
    165175''Centering using median or mean'' - Whether median or mean should be
    166176used for the centering.
    167177
     178''Normalise on gene/assays using median or mean'' - Whether
     179normalisation should be done on genes, assays, or both.
     180
     181''Number of normalization cycles'' - How many cycles should be done
     182during normalisation.
     183
     184''Create debug files'' - If debug data should be stored in `data`
     185directory.
    168186
    169187----------------------------------------------------------------------
    170188{{{
    171 Copyright (C) 2008 Jari Häkkinen
     189Copyright (C) 2008, 2013 Jari Häkkinen
    172190
    173191This file is part of the se.lu.onk.Center plug-in for BASE. Available
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