Changeset 2118

Timestamp:

Nov 5, 2013, 3:44:53 PM (10 years ago)

Author:

Jari Häkkinen

Message:

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

File:

• plugins/base1/se.lu.onk.Center/trunk/README (modified) (9 diffs)

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

@@ -4 +4 @@
 
 The `se.lu.onk.Center` plug-in is a normalisation method where
-expression values are centered around the data median or mean. See
+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 free software. See the file license.txt for
-copying conditions.
-
-The package was created by Johan Enell and is currently maintained by
-Jari Häkkinen.
+`se.lu.onk.Center` is open source software. See the file `license.txt`
+for copying conditions.
+
+The package was created by Johan Enell.
 
 
@@ -23 +22 @@
 == 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.''
+''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
@@ -55 +53 @@
     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
+    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.
@@ -70 +68 @@
 == Compiling ==
 
-You must checkout the `se.lu.onk.Center` from the repository,
+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
@@ -76 +74 @@
 known to work with `se.lu.onk.BaseFile` version 1.0.
 {{{
-  check out project, see instructions below
+  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
@@ -95 +93 @@
 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.
+components, including `BaseFile.jar` and associated files.
 
 
@@ -123 +121 @@
 == Documentation ==
 
-To center your data means that data values are adjusted to reflect
+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 center plug-in allows the user to center the expression
+median. The centre plug-in allows the user to centre the expression
 levels either per gene or per array.
 
@@ -134 +132 @@
 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
+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.
 
-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
+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, labeling efficiency, and image acquisition parameters. Such
+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 centering the data in log-space has the effect
+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
@@ -150 +148 @@
 (or log-ratio of 0).
 
-In general, it is recommended that median rather than mean centering
+In general, it is recommended that median rather than mean centring
 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.
+''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 arrays.
+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 Jari Häkkinen
+Copyright (C) 2008, 2013 Jari Häkkinen
 
 This file is part of the se.lu.onk.Center plug-in for BASE. Available