source: trunk/se/lu/thep/affymetrix/README @ 337

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[123]1$Id: README 294 2007-05-23 12:34:41Z peter $
[123]5Copyright (C) 2006 Jari Häkkinen
[285]6Copyright (C) 2007 Jari Häkkinen, Peter Johansson
[275]8This file is part of package for BASE,
[275] package for BASE is free software; you can
12redistribute it and/or modify it under the terms of the GNU General
13Public License as published by the Free Software Foundation; either
14version 2 of the License, or (at your option) any later version.
[275] package for BASE is distributed in the hope that
17it will be useful, but WITHOUT ANY WARRANTY; without even the implied
19the GNU General Public License for more details.
21You should have received a copy of the GNU General Public License
22along with this program; if not, write to the Free Software
23Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,
[285]28== About package ==
[286]30''A short diversion before we proceed, this paragraph is aimed at
31people starting with an empty BASE server. The default BASE
32installation comes set up to store the same reporter (probeset)
33information as BASE 1.2.x do. This set up is not optimal for
34Affymetrix data but can still be used. In order to understand how to
35define what reporter information is stored in BASE and how to change
36what is stored, you may want to visit
38before you start using your shiny BASE installation.''
[279]40Send comments, suggestion, complaints, or questions regarding this
[285]41package to the
42[ BASE mailing lists].
[275]44This file contains information on package. This
[278]45package contains the RMAExpress and Plier plug-ins.
[285]47The RMAExpress plug-in is installed in the
48[ BASE2 demo server].
[275]50For installation or updating instructions please see file INSTALL.
[285]53== What is RMAExpress and Plier plug-ins for BASE? ==
[276]55RMAExpress and Plier are two similar plug-ins needed to make use of
56Affymetrix data in BASE. Affymetrix data can be imported into BASE as
57files, but if one wants to perform clustering and other analysis
58available in BASE, the data in these files have to be extracted and
59imported into BASE.
[285]61These plug-ins do not implement the RMA method and Plier method, but
62rather rely on third-party binary packages for the algorithm
[276]65The RMAExpress plug-in relies on RMAExpressConsole available in the
66RMAExpress package available at The
67RMA algorithm is published in scientific journals, for more
68information please refer to the RMAExpress web site. In short RMA is
69the Robust Multichip Average. It consists of three steps: a background
[285]70adjustment, quantile normalization, and finally a summarizing.
[276]72The Plier plug-in relies on `apt-probeset-summarize` included in
73Affymetrix Power Tools (APT) available at
[293]75`apt-probeset-summarize` provides several methods and options. For
76time being there is no way to to set these options through the BASE
77GUI. The option `plier-mm` is hard-coded into the plug-in, which
[294]78should be a good choice in most situations. In short the option means
[293]79mismatch probe is used as adjustment for perfect match, quantile
80normalization is done, and PLIER is used for summarizing probesets.
81For more information regarding the PLIER algorithm please refer to the
82Affymetrix home page.
[285]85== What is required for use of these plug-ins for BASE? ==
[285]87This section is a short introduction to get going with the plug-ins
88and Affymetrix data in BASE. More documentation is available at
89 and you should read them to learn
90how to use BASE.
[285]92 1. You need to install the plug-in and make BASE aware of the new
93    plug-in, see INSTALL for instruction for installation instructions.
95 2. You need to import probe set information into BASE (reporter
96    information in BASE language), i.e. import AffyChip_annot.csv into
97    BASE. This is only needed to do once, and optionally later if
98    reporter information should be updated. This step can only be
99    performed by a user with reporter administrative (create)
100    privileges, an ordinary BASE user does NOT have this privilege.
[286]102 There is more than one way to create plug-in configurations. Here we
103 outline the most straightforward route. There is a chapter in the
104 BASE manual devoted for plug-in installation, follow the link above
105 to find the document.
[126]107    - First you need to create an plug-in configuration for the
108      'Reporter importer' plug-in. Locate the 'Reporter importer'
109      plug-in definition ('Administrate' -> 'Plugins' ->
110      'Definitions'). Click on it and choose 'New configuration ...',
111      name the configuration and choose 'Save and configure'.
[126]113    - A 'Parser settings' dialog will appear. Set fields according to
114      this list:
[126]116  Data header  : "Probe Set ID","GeneChip Array",.*
117  Data splitter: (?!"),(?=")
118  Remove quotes: true
119  Name         : \Probe Set ID\
120  Reporter ID  : \Probe Set ID\
122      Finalize by clicking 'Next'. Note, the above example will
123      perform a minimalistic import of annotation information, please
124      read the BASE documentation on how to import more probeset
125      related information. However, don't worry about that now, you
126      can always fix the annotation later.
[126]128    - Import the reporters by choosing 'View' -> 'Reporters' and the
129      clicking on 'Import...'. Click 'Next' without changing the 'auto
[156]130      detect' settings. Supply the file name in the next dialog, click
[126]131      'Next'. Set the 'Update existing reporters' to "true" if an
132      update of already stored reporter information is wanted. Start
[286]133      the import by clicking 'Next' in the parameter dialog.
[286]135 The reporter information is now in the database. You may delete the
136 AffyChip_annot.csv file from BASE if you wish, it is not needed
137 anymore. You may want to update reporter information when Affymetrix
138 releases a new version of their annotation but remember there is no
139 versioning for this type of information in BASE. If you update
140 reporter information you only need to redo the last step.
[286]142 3. You need to define the design of the !AffyChip in BASE,
143    i.e. import the !AffyChip.cdf file. This is only needed to do once
144    for every !AffyChip design to be added into BASE. This step can
145    only be performed by a user with array LIMS administrative
146    (create) privileges, an ordinary BASE user does NOT have this
147    privilege.
[126]149    - Define a new array design through 'Array LIMS' -> 'Array
150      Designs'. Click on 'New ...'. In the 'Create array design'
[285]151      dialog, set the 'Name' (use the file name of the CDF file for
[188]152      convenience), tick the Affy chip tick box, choose a CDF file,
153      and optionally write a description. Click on next, and the new
154      design is created.
156    - Remember to share the design to all users/roles/groups that
157      should have access to it (sharing it to group Everyone should be
[127]158      sufficient in most cases).
[285]160 4. Create an experiment, i.e., grouping .cel files into an
161    experiment.
[127]163    - Upload the .cel files into BASE.
[127]165    - Create raw bio assay for these files, one per file: Choose
166      'View' -> 'Raw bioassays', click on 'New ...'. In the dialog set
167      the 'Name', choose the proper 'Raw data type' (i.e.,
168      "Affymetrix"), choose the 'Array design' that matches the .cel
169      file, and choose the 'CEL file'. (The other fields are not
170      needed but may be handy to fill in.) Click on 'Save'.
172    - Create the experiment: Choose 'View' -> 'Experiment', click on
173      'New ...'. In the dialog set the 'Name', choose the proper 'Raw
174      data type' (i.e., "Affymetrix"), and add 'Raw bioassays'.
[285]176 5. Select the experiment and create a new root bioassay set for it.
178    - Locate the newly created experiment and click on 'Analyze'.
[285]180    - Click on 'New root bioassay set ...', select the algorithm you
181      want to use in the import, and click 'Next' in the pop-up
182      dialog. Select the 'Raw bioassays' to include in the new root
183      bioassay set and type a name for the bioassay set. Click on
[127]184      'Next' to start the plug-in.
[285]186 6. When the plug-in is finished the resulting expression values will
187    be accessible in BASE.
189 7. You made it here. This means that the plug-in works and you are
[286]190    ready to start using BASE. The get the most out of BASE you should
191    now read the BASE manual and documentation available at
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