$Id: README 275 2007-05-21 17:10:55Z peter $

Copyright (C) 2006 Jari Häkkinen
Copyright (C) 2007 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 ==

Send comments, suggestion, complaints, or questions about this document to jari@…

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

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

For installation or updating instructions please see file 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.