Changeset 879


Ignore:
Timestamp:
Dec 5, 2008, 11:28:12 AM (13 years ago)
Author:
Jari Häkkinen
Message:

Changed documentation to document the Center plug-in

File:
1 edited

Legend:

Unmodified
Added
Removed
  • plugins/base1/se.lu.onk.Center/trunk/README

    r875 r879  
    33= About `se.lu.onk.Center` =
    44
    5 The `se.lu.onk.Center` plug-in merge bioassays by grouping them
    6 according to annotation types or syntactical differences in the
    7 name. See ``Documentation`` below fo further information about the
    8 plug-in.
     5The `se.lu.onk.Center` plug-in is a normalisation method where
     6expression values are centered around the data median or mean. See
     7``Documentation`` below for further information about the plug-in.
    98
    109`se.lu.onk.Center` is free software. See the file license.txt for
     
    5150{{{
    5251  # Log in to your BASE as admin
    53   # Upload the configuration file `mergebioassay.base`
     52  # Upload the configuration file misc/plugin_Transformation_Center.base`
    5453  # Create/update a configuration for the plug-in where you select the
    55     plug-in defintion files `mergebioassay.base`. BASE will respond
    56     that plug-ins where configured but ...
     54    plug-in definition file `plugin_Transformation_Center.base`. BASE
     55    will respond that plug-ins where configured but ...
    5756  # Re-configure the plug-in without selecting a file, set the `Plugin
    5857    executables path` and proceed to next window by clicking
     
    124123== Documentation ==
    125124
    126 This plug-in base-users merge bioassays by grouping them according to
    127 annotation types or syntactical differences in the name. There are
    128 four different methods for calculating the merged values. They differ
    129 in what kind of mean they are using (arithmetic or geometric) and if
    130 they are merging on ratio or intensity.
     125To center your data means that data values are adjusted to reflect
     126their variation from some property of the data such as the mean or
     127median. The center plug-in allows the user to center the expression
     128levels either per gene or per array.
    131129
    132 For each group the parents are saved so the link to the raw data is
    133 preserved. Annotations for the bioassays are saved if sample1 is the
    134 same for each assay in each group.
     130Consider a common experimental design where you are looking at a large
     131number of samples all compared to a common reference. For each gene,
     132you have a series of ratio values that are relative to the expression
     133level of that gene in the reference sample. Since the reference sample
     134really has nothing to do with your experiment, you want your analysis
     135to be independent of the amount of a gene present in the reference
     136sample. This is achieved by center your data on genes. Centering makes
     137less sense in experiments where the reference sample is part of the
     138experiment.
    135139
    136 === Merge methods ===
     140Centering the data for arrays can also be used to remove certain types
     141of bias and can be seen as a crude normalization. The results of many
     142two-color fluorescent hybridization experiments are not corrected for
     143systematic biases in ratios that are the result of differences in RNA
     144amounts, labeling efficiency, and image acquisition parameters. Such
     145bias have the effect of multiplying ratios for all genes by a fixed
     146scalar. Mean or median centering the data in log-space has the effect
     147of correcting this bias, although it should be noted that an
     148assumption is being made in correcting this bias, which is that the
     149average gene in a given experiment is expected to have a ratio of 1.0
     150(or log-ratio of 0).
    137151
    138 ''Geometric mean of ratio''::
    139   This method calculates the geometric mean of the ratios in each
    140   group per position.
    141 
    142 ''Arithmetic mean of ratio''::
    143   This method calculates the arithmetic mean of the ratios in each
    144   group per position.
    145 
    146 ''Arithmetic mean of intensity''::
    147   This method calculates the arithmetic mean of the intensities in
    148   each group per position.
    149 
    150 ''Ratio of ratio''::
    151   This method works a little bit different from the others. It
    152   requires that each group consists of exactly two bioassays. It will
    153   then create a new ratio for each spot with one of the assays over
    154   the other, depending on what the user has specified in the ratio
    155   parameters.
     152In general, it is recommended that median rather than mean centering
     153is used since it is more robust against outliers.
    156154
    157155=== Parameters ===
    158156
    159 ''Assayname''::
    160   This parameter specifies how the name of the assays is
    161   constructed. Use %0-%9 as wildcards and then put any character(s)
    162   between as delimiters. For example assay name Assay_1_A can be
    163   divided into three parts. By setting the parameter to %1_%2_%3 the
    164   plugin will read assay name assay_1_A and set %1=Assay, %2=1 and
    165   %3=A. Thus, if your assays have names constructed in the same way
    166   merge can sort the assays in groups depending on %1, %2 or %3.
     157''Center on genes/arrays'' - Whether centering should be done on
     158genes, arrays or both. If both is chosen then the centering will first
     159be done on genes then on arrays, this is called a cycle.
    167160
    168 ''Group''::
    169   This will specify how the assays will be grouped together. It can
    170   either be a %-number used in assayname or an annotation type.
     161''Number of centering cycles'' - How many cycles should be done during
     162centering. This value is only relevant if the centering should be done
     163on both genes and arrays.
    171164
    172   Example 1: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can
    173   be sorted into groups of assays using merge.
    174 
    175   A: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter
    176   \221Group\222 = %2 will sort the assays into two groups.
    177 {{{
    178 One group were %2=1  (assays Assay_1_A and Assay_1_B)
    179 One group were %2=2  (assays Assay_2_A and Assay_2_B)
    180 }}}
    181   B: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter
    182   \221Group\222 = %3 will sort the assays into two groups.
    183 {{{
    184 One group were %3=A  (assays Assay_1_A and Assay_2_A)
    185 One group were %3=B  (assays Assay_1_B and Assay_1_B)
    186 }}}
    187 
    188 ''New name''::
    189   This text will be used in the name of the merged assays. The name
    190   will be this string followed by the groupname.
    191 
    192 ''Merge method''::
    193   Choose one of the methodes described above.
    194 
    195 ''Ratio''::
    196   If merge method `ratio of ratio` is chosen the form of the ratio
    197   must be specified. This is done either in the ratio parameter or in
    198   ratio annotation type and ratio annotation value. In the ratio
    199   parameter you can choose a %-number followed by the two values it
    200   can take. The last character in the string must be the delimiter the
    201   user has choosen ot use. The other way a user can specify the ratio
    202   is by choosing an annotation type in the list and specify the values
    203   in the annotation values parameter. This is done by writing the
    204   values with the delimiter used last,
    205 {{{
    206 %1|vr1|vr2|
    207 }}}
    208   This will take the values from %1 in the assayname and put the assay
    209   with value vr1 over the assay with values vr2. Notice that the final
    210   character is the delimiter (this can of course be any character).
    211 
    212   Example 2: Assays; Assay_1_A, Assay_2_A, Assay_1_B and Assay_2_B can be
    213   sorted into groups of assays using merge.
    214 
    215   A: Setting the parameter \221Assayname\222 = %1_%2_%3 and parameter
    216   \221Group\222 = %2 will sort the assays into two groups.
    217 {{{
    218 One group were %2=1  (assays Assay_1_A and Assay_1_B)
    219 One group were %2=2  (assays Assay_2_A and Assay_2_B)
    220 }}}
    221   B: By setting parameter \221Ratio\222 = %3|A|B| ratios of ratios
    222   will be created as:
    223 {{{
    224 Assay_1_A / Assay_1_B
    225 Assay_2_A / Assay_2_B
    226 }}}
    227 
    228 === References ===
    229 
    230 [http://mathworld.wolfram.com/ArithmeticMean.html Arithmetic mean] [[br]]
    231 [http://mathworld.wolfram.com/GeometricMean.html Geometric mean]
     165''Centering using median or mean'' - Whether median or mean should be
     166used for the centering.
    232167
    233168
Note: See TracChangeset for help on using the changeset viewer.