source: trunk/se/lu/thep/affymetrix/README @ 337

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

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{{{
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
[http://base.thep.lu.se/wiki/MailingLists 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
[http://base2.thep.lu.se:8080/demo 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.

 2. 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.

 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 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).

 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 ...', 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.

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

 7. 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