source: trunk/se/lu/thep/affymetrix/README @ 188

$Id: README 188 2006-10-26 11:03:45Z jari $

======================================================================
Copyright (C) 2006 Jari Häkkinen

This file is part of RMAExpress plug-in for BASE,
http://baseplugins.thep.lu.se/wiki/thep.lu.se.RMAExpress

RMAExpress plug-in 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.

RMAExpress plug-in 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.
======================================================================


Send comments, suggestion, complaints, or questions about this
document to jari@thep.lu.se


The plug-in is installed in the BASE2 demo server
(http://lev.thep.lu.se/base2demo).


For installation or updating instructions please see INSTALL.


What is RMAExpress plug-in for BASE?

Currently, this is a tool 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. There
may (and probably will) be other ways to analyze Affymetrix data in
BASE in the future.

This plug-in do not implement the RMA method itself but rather 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 summarization.


What is required to use the RMAExpress plug-in for BASE? The "BASE
getting started document" may also be helpful,
http://base.thep.lu.se/chrome/site/doc/user/getting_started.html

1) You need to install the plug-in and make BASE aware of the new
   plugin, see INSTALL for instruction for installation
   instructions.

2) You need to import probe set information into BASE (reporter
   information), 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.

    - 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'.

    - 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.

3) 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 filename 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).

4) 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'.

5) 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 ...' 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.

6) When the plug-in is finished the resulting expression values will
   be accessible in BASE.