source: trunk/se/lu/thep/affymetrix/README @ 350

Last change on this file since 350 was 345, checked in by Jari Häkkinen, 15 years ago

Fixes #67 and #68. Added information on how to install in Microsoft Windows. Also improved the docs.

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File size: 8.7 KB
[123]1$Id: README 345 2007-06-27 19:47:01Z jari $
[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
[286]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.
[345]47The plug-ins in this package are installed in the
48[ BASE2 demo server]. You can try
49them there before deciding to install them in your local BASE server.
[275]51For installation or updating instructions please see file INSTALL.
[285]54== What is RMAExpress and Plier plug-ins for BASE? ==
[276]56RMAExpress and Plier are two similar plug-ins needed to make use of
57Affymetrix data in BASE. Affymetrix data can be imported into BASE as
58files, but if one wants to perform clustering and other analysis
59available in BASE, the data in these files have to be extracted and
60imported into BASE.
[285]62These plug-ins do not implement the RMA method and Plier method, but
63rather rely on third-party binary packages for the algorithm
[276]66The RMAExpress plug-in relies on RMAExpressConsole available in the
67RMAExpress package available at The
68RMA algorithm is published in scientific journals, for more
69information please refer to the RMAExpress web site. In short RMA is
70the Robust Multichip Average. It consists of three steps: a background
[285]71adjustment, quantile normalization, and finally a summarizing.
[276]73The Plier plug-in relies on `apt-probeset-summarize` included in
74Affymetrix Power Tools (APT) available at
[293]76`apt-probeset-summarize` provides several methods and options. For
77time being there is no way to to set these options through the BASE
78GUI. The option `plier-mm` is hard-coded into the plug-in, which
[294]79should be a good choice in most situations. In short the option means
[293]80mismatch probe is used as adjustment for perfect match, quantile
81normalization is done, and PLIER is used for summarizing probesets.
82For more information regarding the PLIER algorithm please refer to the
83Affymetrix home page.
[285]86== What is required for use of these plug-ins for BASE? ==
[285]88This section is a short introduction to get going with the plug-ins
89and Affymetrix data in BASE. More documentation is available at
[345]90 and you should read them to learn how to use
[285]93 1. You need to install the plug-in and make BASE aware of the new
94    plug-in, see INSTALL for instruction for installation instructions.
96 2. You need to import probe set information into BASE (reporter
97    information in BASE language), i.e. import AffyChip_annot.csv into
98    BASE. This is only needed to do once, and optionally later if
99    reporter information should be updated. This step can only be
100    performed by a user with reporter administrative (create)
101    privileges, an ordinary BASE user does NOT have this privilege.
[345]103    There is more than one way to create plug-in configurations. Here
104    we outline the most straightforward route. There is a chapter in
105    the BASE manual devoted for plug-in installation, follow the link
106    above to find the document.
[126]108    - First you need to create an plug-in configuration for the
109      'Reporter importer' plug-in. Locate the 'Reporter importer'
110      plug-in definition ('Administrate' -> 'Plugins' ->
111      'Definitions'). Click on it and choose 'New configuration ...',
112      name the configuration and choose 'Save and configure'.
[126]114    - A 'Parser settings' dialog will appear. Set fields according to
115      this list:
[126]117  Data header  : "Probe Set ID","GeneChip Array",.*
118  Data splitter: (?!"),(?=")
119  Remove quotes: true
120  Name         : \Probe Set ID\
121  Reporter ID  : \Probe Set ID\
123      Finalize by clicking 'Next'. Note, the above example will
124      perform a minimalistic import of annotation information, please
125      read the BASE documentation on how to import more probeset
126      related information. However, don't worry about that now, you
127      can always fix the annotation later.
[126]129    - Import the reporters by choosing 'View' -> 'Reporters' and the
130      clicking on 'Import...'. Click 'Next' without changing the 'auto
[156]131      detect' settings. Supply the file name in the next dialog, click
[126]132      'Next'. Set the 'Update existing reporters' to "true" if an
133      update of already stored reporter information is wanted. Start
[286]134      the import by clicking 'Next' in the parameter dialog.
[345]136    The reporter information is now in the database. You may delete
137    the AffyChip_annot.csv file from BASE if you wish, it is not
138    needed anymore. You may want to update reporter information when
139    Affymetrix releases a new version of their annotation but remember
140    there is no versioning for this type of information in BASE. If
141    you update reporter information you only need to redo the last
142    step.
[286]144 3. You need to define the design of the !AffyChip in BASE,
145    i.e. import the !AffyChip.cdf file. This is only needed to do once
146    for every !AffyChip design to be added into BASE. This step can
147    only be performed by a user with array LIMS administrative
148    (create) privileges, an ordinary BASE user does NOT have this
149    privilege.
[126]151    - Define a new array design through 'Array LIMS' -> 'Array
152      Designs'. Click on 'New ...'. In the 'Create array design'
[285]153      dialog, set the 'Name' (use the file name of the CDF file for
[188]154      convenience), tick the Affy chip tick box, choose a CDF file,
155      and optionally write a description. Click on next, and the new
156      design is created.
158    - Remember to share the design to all users/roles/groups that
159      should have access to it (sharing it to group Everyone should be
[127]160      sufficient in most cases).
[285]162 4. Create an experiment, i.e., grouping .cel files into an
163    experiment.
[127]165    - Upload the .cel files into BASE.
[127]167    - Create raw bio assay for these files, one per file: Choose
168      'View' -> 'Raw bioassays', click on 'New ...'. In the dialog set
169      the 'Name', choose the proper 'Raw data type' (i.e.,
170      "Affymetrix"), choose the 'Array design' that matches the .cel
171      file, and choose the 'CEL file'. (The other fields are not
172      needed but may be handy to fill in.) Click on 'Save'.
174    - Create the experiment: Choose 'View' -> 'Experiment', click on
175      'New ...'. In the dialog set the 'Name', choose the proper 'Raw
176      data type' (i.e., "Affymetrix"), and add 'Raw bioassays'.
[285]178 5. Select the experiment and create a new root bioassay set for it.
180    - Locate the newly created experiment and click on 'Analyze'.
[285]182    - Click on 'New root bioassay set ...', select the algorithm you
183      want to use in the import, and click 'Next' in the pop-up
184      dialog. Select the 'Raw bioassays' to include in the new root
185      bioassay set and type a name for the bioassay set. Click on
[127]186      'Next' to start the plug-in.
[285]188 6. When the plug-in is finished the resulting expression values will
189    be accessible in BASE.
191 7. You made it here. This means that the plug-in works and you are
[345]192    ready to start using Affymetrix data in BASE. The get the most out
193    of BASE you should now read the BASE manual and documentation
194    available at
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