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$Id: README 294 2007-05-23 12:34:41Z peter $


Copyright (C) 2006 Jari Häkkinen
Copyright (C) 2007 Jari Häkkinen, Peter Johansson
This file is part of se.lu.thep.affymetrix package for BASE,
http://baseplugins.thep.lu.se/wiki/se.thep.lu.se.affymetrix
se.lu.thep.affymetrix package for BASE is free software; you can
redistribute it and/or modify it under the terms of the GNU General
Public License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
se.lu.thep.affymetrix package for BASE is distributed in the hope that
it will be useful, but WITHOUT ANY WARRANTY; without even the implied
warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See
the GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,
USA.

About se.lu.thep.affymetrix package

A short diversion before we proceed, this paragraph is aimed at people starting with an empty BASE server. The default BASE installation comes set up to store the same reporter (probeset) information as BASE 1.2.x do. This set up is not optimal for Affymetrix data but can still be used. In order to understand how to define what reporter information is stored in BASE and how to change what is stored, you may want to visit http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html before you start using your shiny BASE installation.

Send comments, suggestion, complaints, or questions regarding this package to the BASE mailing lists.

This file contains information on se.lu.thep.affymetrix package. This package contains the RMAExpress and Plier plug-ins.

The RMAExpress plug-in is installed in the BASE2 demo server.

For installation or updating instructions please see file INSTALL.

What is RMAExpress and Plier plug-ins for BASE?

RMAExpress and Plier are two similar plug-ins needed to make use of Affymetrix data in BASE. Affymetrix data can be imported into BASE as files, but if one wants to perform clustering and other analysis available in BASE, the data in these files have to be extracted and imported into BASE.

These plug-ins do not implement the RMA method and Plier method, but rather rely on third-party binary packages for the algorithm implementations.

The RMAExpress plug-in relies on RMAExpressConsole available in the RMAExpress package available at http://rmaexpress.bmbolstad.com/. The RMA algorithm is published in scientific journals, for more information please refer to the RMAExpress web site. In short RMA is the Robust Multichip Average. It consists of three steps: a background adjustment, quantile normalization, and finally a summarizing.

The Plier plug-in relies on apt-probeset-summarize included in Affymetrix Power Tools (APT) available at http://www.affymetrix.com/support/developer/powertools/index.affx. apt-probeset-summarize provides several methods and options. For time being there is no way to to set these options through the BASE GUI. The option plier-mm is hard-coded into the plug-in, which should be a good choice in most situations. In short the option means mismatch probe is used as adjustment for perfect match, quantile normalization is done, and PLIER is used for summarizing probesets. For more information regarding the PLIER algorithm please refer to the Affymetrix home page.

What is required for use of these plug-ins for BASE?

This section is a short introduction to get going with the plug-ins and Affymetrix data in BASE. More documentation is available at http://base.thep.lu.se/wiki/Manuals and you should read them to learn how to use BASE.

  1. You need to install the plug-in and make BASE aware of the new plug-in, see INSTALL for instruction for installation instructions.
  1. You need to import probe set information into BASE (reporter information in BASE language), i.e. import AffyChip_annot.csv into BASE. This is only needed to do once, and optionally later if reporter information should be updated. This step can only be performed by a user with reporter administrative (create) privileges, an ordinary BASE user does NOT have this privilege.

There is more than one way to create plug-in configurations. Here we outline the most straightforward route. There is a chapter in the BASE manual devoted for plug-in installation, follow the link above to find the document.

  • First you need to create an plug-in configuration for the 'Reporter importer' plug-in. Locate the 'Reporter importer' plug-in definition ('Administrate' -> 'Plugins' -> 'Definitions'). Click on it and choose 'New configuration ...', name the configuration and choose 'Save and configure'.
  • A 'Parser settings' dialog will appear. Set fields according to this list:
    	Data header  : "Probe Set ID","GeneChip Array",.*
    	Data splitter: (?!"),(?=")
    	Remove quotes: true
    	Name         : \Probe Set ID\
    	Reporter ID  : \Probe Set ID\
    
    Finalize by clicking 'Next'. Note, the above example will perform a minimalistic import of annotation information, please read the BASE documentation on how to import more probeset related information. However, don't worry about that now, you can always fix the annotation later.
  • Import the reporters by choosing 'View' -> 'Reporters' and the clicking on 'Import...'. Click 'Next' without changing the 'auto detect' settings. Supply the file name in the next dialog, click 'Next'. Set the 'Update existing reporters' to "true" if an update of already stored reporter information is wanted. Start the import by clicking 'Next' in the parameter dialog.

The reporter information is now in the database. You may delete the AffyChip_annot.csv file from BASE if you wish, it is not needed anymore. You may want to update reporter information when Affymetrix releases a new version of their annotation but remember there is no versioning for this type of information in BASE. If you update reporter information you only need to redo the last step.

  1. You need to define the design of the AffyChip in BASE, i.e. import the AffyChip.cdf file. This is only needed to do once for every AffyChip design to be added into BASE. This step can only be performed by a user with array LIMS administrative (create) privileges, an ordinary BASE user does NOT have this privilege.
  • Define a new array design through 'Array LIMS' -> 'Array Designs'. Click on 'New ...'. In the 'Create array design' dialog, set the 'Name' (use the file name of the CDF file for convenience), tick the Affy chip tick box, choose a CDF file, and optionally write a description. Click on next, and the new design is created.
  • Remember to share the design to all users/roles/groups that should have access to it (sharing it to group Everyone should be sufficient in most cases).
  1. Create an experiment, i.e., grouping .cel files into an experiment.
  • Upload the .cel files into BASE.
  • Create raw bio assay for these files, one per file: Choose 'View' -> 'Raw bioassays', click on 'New ...'. In the dialog set the 'Name', choose the proper 'Raw data type' (i.e., "Affymetrix"), choose the 'Array design' that matches the .cel file, and choose the 'CEL file'. (The other fields are not needed but may be handy to fill in.) Click on 'Save'.
  • Create the experiment: Choose 'View' -> 'Experiment', click on 'New ...'. In the dialog set the 'Name', choose the proper 'Raw data type' (i.e., "Affymetrix"), and add 'Raw bioassays'.
  1. Select the experiment and create a new root bioassay set for it.
  • Locate the newly created experiment and click on 'Analyze'.
  • Click on 'New root bioassay set ...', select the algorithm you want to use in the import, and click 'Next' in the pop-up dialog. Select the 'Raw bioassays' to include in the new root bioassay set and type a name for the bioassay set. Click on 'Next' to start the plug-in.
  1. When the plug-in is finished the resulting expression values will be accessible in BASE.
  1. You made it here. This means that the plug-in works and you are ready to start using BASE. The get the most out of BASE you should now read the BASE manual and documentation available at http://base.thep.lu.se/wiki/Manuals
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