source: trunk/se/lu/thep/affymetrix/README @ 285

Last change on this file since 285 was 285, checked in by Jari Häkkinen, 16 years ago

Addresses #42.

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[123]1$Id: README 285 2007-05-22 12:51:46Z 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 ==
[279]30Send comments, suggestion, complaints, or questions regarding this
[285]31package to the
32[ BASE mailing lists].
[275]34This file contains information on package. This
[278]35package contains the RMAExpress and Plier plug-ins.
[285]37The RMAExpress plug-in is installed in the
38[ BASE2 demo server].
[275]41For installation or updating instructions please see file INSTALL.
[285]44== What is RMAExpress and Plier plug-ins for BASE? ==
[276]46RMAExpress and Plier are two similar plug-ins needed to make use of
47Affymetrix data in BASE. Affymetrix data can be imported into BASE as
48files, but if one wants to perform clustering and other analysis
49available in BASE, the data in these files have to be extracted and
50imported into BASE.
[285]52These plug-ins do not implement the RMA method and Plier method, but
53rather rely on third-party binary packages for the algorithm
[276]56The RMAExpress plug-in relies on RMAExpressConsole available in the
57RMAExpress package available at The
58RMA algorithm is published in scientific journals, for more
59information please refer to the RMAExpress web site. In short RMA is
60the Robust Multichip Average. It consists of three steps: a background
[285]61adjustment, quantile normalization, and finally a summarizing.
[276]63The Plier plug-in relies on `apt-probeset-summarize` included in
64Affymetrix Power Tools (APT) available at
66`apt-probeset-summarize` provides several methods (see Affymetrix home
67page). Here we use the method given with option flag `--option
[277]68plier-mm`. For more information regarding the Plier algorithm please
69refer to the Affymetrix home page.
[285]72== What is required for use of these plug-ins for BASE? ==
[285]74This section is a short introduction to get going with the plug-ins
75and Affymetrix data in BASE. More documentation is available at
76 and you should read them to learn
77how to use BASE.
[285]79 1. You need to install the plug-in and make BASE aware of the new
80    plug-in, see INSTALL for instruction for installation instructions.
82 2. You need to import probe set information into BASE (reporter
83    information in BASE language), i.e. import AffyChip_annot.csv into
84    BASE. This is only needed to do once, and optionally later if
85    reporter information should be updated. This step can only be
86    performed by a user with reporter administrative (create)
87    privileges, an ordinary BASE user does NOT have this privilege.
89    There is more than one way to create plug-in configurations. Here
90    we outline the most straightforward route. There is a chapter in
91    the BASE manual devoted for plug-in installation, follow the link
92    above to find the document.
[126]94    - First you need to create an plug-in configuration for the
95      'Reporter importer' plug-in. Locate the 'Reporter importer'
96      plug-in definition ('Administrate' -> 'Plugins' ->
97      'Definitions'). Click on it and choose 'New configuration ...',
98      name the configuration and choose 'Save and configure'.
[126]100    - A 'Parser settings' dialog will appear. Set fields according to
101      this list:
[126]103  Data header  : "Probe Set ID","GeneChip Array",.*
104  Data splitter: (?!"),(?=")
105  Remove quotes: true
106  Name         : \Probe Set ID\
107  Reporter ID  : \Probe Set ID\
109      Finalize by clicking 'Next'. Note, the above example will
110      perform a minimalistic import of annotation information, please
111      read the BASE documentation on how to import more probeset
112      related information. However, don't worry about that now, you
113      can always fix the annotation later.
[126]115    - Import the reporters by choosing 'View' -> 'Reporters' and the
116      clicking on 'Import...'. Click 'Next' without changing the 'auto
[156]117      detect' settings. Supply the file name in the next dialog, click
[126]118      'Next'. Set the 'Update existing reporters' to "true" if an
119      update of already stored reporter information is wanted. Start
120      the import by clicking 'Next' in the parameter dialog
[126]122   The reporter information is now in the database. You may delete the
123   AffyChip_annot.csv file from BASE if you wish, it is not needed
124   anymore. You may want to update reporter information when
125   Affymetrix releases a new version of their annotation but remember
126   there is no versioning for this type of information in BASE. If you
127   update reporter information you only need to redo the last step.
[285]129 3. You need to define the design of the AffyChip in BASE, i.e. import
130    the AffyChip.cdf file. This is only needed to do once for every
131    AffyChip design to be added into BASE. This step can only be
132    performed by a user with array LIMS administrative (create)
133    privileges, an ordinary BASE user does NOT have this privilege.
[126]135    - Define a new array design through 'Array LIMS' -> 'Array
136      Designs'. Click on 'New ...'. In the 'Create array design'
[285]137      dialog, set the 'Name' (use the file name of the CDF file for
[188]138      convenience), tick the Affy chip tick box, choose a CDF file,
139      and optionally write a description. Click on next, and the new
140      design is created.
142    - Remember to share the design to all users/roles/groups that
143      should have access to it (sharing it to group Everyone should be
[127]144      sufficient in most cases).
[285]146 4. Create an experiment, i.e., grouping .cel files into an
147    experiment.
[127]149    - Upload the .cel files into BASE.
[127]151    - Create raw bio assay for these files, one per file: Choose
152      'View' -> 'Raw bioassays', click on 'New ...'. In the dialog set
153      the 'Name', choose the proper 'Raw data type' (i.e.,
154      "Affymetrix"), choose the 'Array design' that matches the .cel
155      file, and choose the 'CEL file'. (The other fields are not
156      needed but may be handy to fill in.) Click on 'Save'.
158    - Create the experiment: Choose 'View' -> 'Experiment', click on
159      'New ...'. In the dialog set the 'Name', choose the proper 'Raw
160      data type' (i.e., "Affymetrix"), and add 'Raw bioassays'.
[285]162 5. Select the experiment and create a new root bioassay set for it.
164    - Locate the newly created experiment and click on 'Analyze'.
[285]166    - Click on 'New root bioassay set ...', select the algorithm you
167      want to use in the import, and click 'Next' in the pop-up
168      dialog. Select the 'Raw bioassays' to include in the new root
169      bioassay set and type a name for the bioassay set. Click on
[127]170      'Next' to start the plug-in.
[285]172 6. When the plug-in is finished the resulting expression values will
173    be accessible in BASE.
175 7. You made it here. This means that the plug-in works and you are
176    ready to start using BASE. The get the most out of BASE you should
177    now read the BASE manual and documentation available at
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