source: trunk/se/lu/thep/affymetrix/README @ 275

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[123]1$Id: README 275 2007-05-21 17:10:55Z peter $
[123]5Copyright (C) 2006 Jari Häkkinen
[275]6Copyright (C) 2007 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,
[275]28= About package ===
30Send comments, suggestion, complaints, or questions about this
31document to
[275]33This file contains information on package. This
34package contain the RMAExpress and Plier plug-ins.
[275]36The RMAExpress plug-in is installed in the BASE2 demo server
[275]40For installation or updating instructions please see file INSTALL.
[124]43What is RMAExpress plug-in for BASE?
[124]45Currently, this is a tool needed to make use of Affymetrix data in
[123]46BASE. Affymetrix data can be imported into BASE as files, but if one
[124]47wants to perform clustering and other analysis available in BASE, the
48data in these files have to be extracted and imported into BASE. There
49may (and probably will) be other ways to analyze Affymetrix data in
50BASE in the future.
[124]52This plug-in do not implement the RMA method itself but rather relies
53on RMAExpressConsole available in the RMAExpress package available at
54 The RMA algorithm is published in
55scientific journals, for more information please refer to the
56RMAExpress web site. In short RMA is the Robust Multichip Average. It
57consists of three steps: a background adjustment, quantile
58normalization, and finally a summarization.
[188]61What is required to use the RMAExpress plug-in for BASE? The "BASE
62getting started document" may also be helpful,
[125]651) You need to install the plug-in and make BASE aware of the new
66   plugin, see INSTALL for instruction for installation
67   instructions.
692) You need to import probe set information into BASE (reporter
[125]70   information), i.e. import AffyChip_annot.csv into BASE. This is
71   only needed to do once, and optionally later if reporter
[126]72   information should be updated. This step can only be performed by a
[156]73   user with reporter administrative (create) privileges, an ordinary
[126]74   BASE user does NOT have this privilege.
[126]76    - First you need to create an plug-in configuration for the
77      'Reporter importer' plug-in. Locate the 'Reporter importer'
78      plug-in definition ('Administrate' -> 'Plugins' ->
79      'Definitions'). Click on it and choose 'New configuration ...',
80      name the configuration and choose 'Save and configure'.
[126]82    - A 'Parser settings' dialog will appear. Set fields according to
83      this list:
[126]85  Data header  : "Probe Set ID","GeneChip Array",.*
86  Data splitter: (?!"),(?=")
87  Remove quotes: true
88  Name         : \Probe Set ID\
89  Reporter ID  : \Probe Set ID\
[126]91      Finalize by clicking 'Next'.
[126]93    - Import the reporters by choosing 'View' -> 'Reporters' and the
94      clicking on 'Import...'. Click 'Next' without changing the 'auto
[156]95      detect' settings. Supply the file name in the next dialog, click
[126]96      'Next'. Set the 'Update existing reporters' to "true" if an
97      update of already stored reporter information is wanted. Start
98      the import by clicking 'Next' in the parameter dialog
[126]100   The reporter information is now in the database. You may delete the
101   AffyChip_annot.csv file from BASE if you wish, it is not needed
102   anymore. You may want to update reporter information when
103   Affymetrix releases a new version of their annotation but remember
104   there is no versioning for this type of information in BASE. If you
105   update reporter information you only need to redo the last step.
[123]1073) You need to define the design of the AffyChip in BASE, i.e. import
[126]108   the AffyChip.cdf file. This is only needed to do once for every
109   AffyChip design to be added into BASE. This step can only be
110   performed by a user with array LIMS administrative (create)
[156]111   privileges, an ordinary BASE user does NOT have this privilege.
[126]113    - Define a new array design through 'Array LIMS' -> 'Array
114      Designs'. Click on 'New ...'. In the 'Create array design'
[188]115      dialog, set the 'Name' (use the filename of the CDF file for
116      convenience), tick the Affy chip tick box, choose a CDF file,
117      and optionally write a description. Click on next, and the new
118      design is created.
120    - Remember to share the design to all users/roles/groups that
121      should have access to it (sharing it to group Everyone should be
[127]122      sufficient in most cases).
[127]1244) Create an experiment, i.e., grouping .cel files into an experiment.
[127]126    - Upload the .cel files into BASE.
[127]128    - Create raw bio assay for these files, one per file: Choose
129      'View' -> 'Raw bioassays', click on 'New ...'. In the dialog set
130      the 'Name', choose the proper 'Raw data type' (i.e.,
131      "Affymetrix"), choose the 'Array design' that matches the .cel
132      file, and choose the 'CEL file'. (The other fields are not
133      needed but may be handy to fill in.) Click on 'Save'.
135    - Create the experiment: Choose 'View' -> 'Experiment', click on
136      'New ...'. In the dialog set the 'Name', choose the proper 'Raw
137      data type' (i.e., "Affymetrix"), and add 'Raw bioassays'.
1395) Select the experiment and create a new root bioassay set for it.
141    - Locate the newly created experiment and click on 'Analyze'.
143    - Click on 'New root bioassay set ...' and click 'Next' in the
144      pop-up dialog. Select the 'Raw bioassays' to include in the new
145      root bioassay set and type a name for the bioassay set. Click on
146      'Next' to start the plug-in.
1486) When the plug-in is finished the resulting expression values will
149   be accessible in BASE.
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