source: trunk/se/lu/thep/affymetrix/README @ 276

Last change on this file since 276 was 276, checked in by Peter Johansson, 16 years ago

updated README for affy package refs #45

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[123]1$Id: README 276 2007-05-21 17:44:04Z 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,
[276]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.
[276]43What is RMAExpress and Plier plug-ins for BASE?
[276]45RMAExpress and Plier are two similar plug-ins needed to make use of
46Affymetrix data in BASE. Affymetrix data can be imported into BASE as
47files, but if one wants to perform clustering and other analysis
48available in BASE, the data in these files have to be extracted and
49imported into BASE.
[276]51These plug-ins do not implement the RMA method and Plier method,
52respectively, but rather relies on third-party binary packages.
[276]54The RMAExpress plug-in relies on RMAExpressConsole available in the
55RMAExpress package available at The
56RMA algorithm is published in scientific journals, for more
57information please refer to the RMAExpress web site. In short RMA is
58the Robust Multichip Average. It consists of three steps: a background
59adjustment, quantile normalization, and finally a summarization.
[276]61The Plier plug-in relies on `apt-probeset-summarize` included in
62Affymetrix Power Tools (APT) available at
64`apt-probeset-summarize` provides several methods (see Affymetrix home
65page). Here we use the method given with option flag `--option
68What is required to use the these plug-ins for BASE? The "BASE
[188]69getting started document" may also be helpful,
[125]721) You need to install the plug-in and make BASE aware of the new
73   plugin, see INSTALL for instruction for installation
74   instructions.
762) You need to import probe set information into BASE (reporter
[125]77   information), i.e. import AffyChip_annot.csv into BASE. This is
78   only needed to do once, and optionally later if reporter
[126]79   information should be updated. This step can only be performed by a
[156]80   user with reporter administrative (create) privileges, an ordinary
[126]81   BASE user does NOT have this privilege.
[126]83    - First you need to create an plug-in configuration for the
84      'Reporter importer' plug-in. Locate the 'Reporter importer'
85      plug-in definition ('Administrate' -> 'Plugins' ->
86      'Definitions'). Click on it and choose 'New configuration ...',
87      name the configuration and choose 'Save and configure'.
[126]89    - A 'Parser settings' dialog will appear. Set fields according to
90      this list:
[126]92  Data header  : "Probe Set ID","GeneChip Array",.*
93  Data splitter: (?!"),(?=")
94  Remove quotes: true
95  Name         : \Probe Set ID\
96  Reporter ID  : \Probe Set ID\
[126]98      Finalize by clicking 'Next'.
[126]100    - Import the reporters by choosing 'View' -> 'Reporters' and the
101      clicking on 'Import...'. Click 'Next' without changing the 'auto
[156]102      detect' settings. Supply the file name in the next dialog, click
[126]103      'Next'. Set the 'Update existing reporters' to "true" if an
104      update of already stored reporter information is wanted. Start
105      the import by clicking 'Next' in the parameter dialog
[126]107   The reporter information is now in the database. You may delete the
108   AffyChip_annot.csv file from BASE if you wish, it is not needed
109   anymore. You may want to update reporter information when
110   Affymetrix releases a new version of their annotation but remember
111   there is no versioning for this type of information in BASE. If you
112   update reporter information you only need to redo the last step.
[123]1143) You need to define the design of the AffyChip in BASE, i.e. import
[126]115   the AffyChip.cdf file. This is only needed to do once for every
116   AffyChip design to be added into BASE. This step can only be
117   performed by a user with array LIMS administrative (create)
[156]118   privileges, an ordinary BASE user does NOT have this privilege.
[126]120    - Define a new array design through 'Array LIMS' -> 'Array
121      Designs'. Click on 'New ...'. In the 'Create array design'
[188]122      dialog, set the 'Name' (use the filename of the CDF file for
123      convenience), tick the Affy chip tick box, choose a CDF file,
124      and optionally write a description. Click on next, and the new
125      design is created.
127    - Remember to share the design to all users/roles/groups that
128      should have access to it (sharing it to group Everyone should be
[127]129      sufficient in most cases).
[127]1314) Create an experiment, i.e., grouping .cel files into an experiment.
[127]133    - Upload the .cel files into BASE.
[127]135    - Create raw bio assay for these files, one per file: Choose
136      'View' -> 'Raw bioassays', click on 'New ...'. In the dialog set
137      the 'Name', choose the proper 'Raw data type' (i.e.,
138      "Affymetrix"), choose the 'Array design' that matches the .cel
139      file, and choose the 'CEL file'. (The other fields are not
140      needed but may be handy to fill in.) Click on 'Save'.
142    - Create the experiment: Choose 'View' -> 'Experiment', click on
143      'New ...'. In the dialog set the 'Name', choose the proper 'Raw
144      data type' (i.e., "Affymetrix"), and add 'Raw bioassays'.
1465) Select the experiment and create a new root bioassay set for it.
148    - Locate the newly created experiment and click on 'Analyze'.
150    - Click on 'New root bioassay set ...' and click 'Next' in the
151      pop-up dialog. Select the 'Raw bioassays' to include in the new
152      root bioassay set and type a name for the bioassay set. Click on
153      'Next' to start the plug-in.
1556) When the plug-in is finished the resulting expression values will
156   be accessible in BASE.
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