source: plugins/base2/net.sf.basedb.agilent/trunk/README @ 1215

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$Id: README 1199 2010-03-06 08:54:15Z jari $


  1. BASE 2.14.0 or later.


This file contains general information about the plug-in package and specific information about expression data.

The Agilent plug-ins for BASE will add support for Agilent 1-channel expression data to your BASE server. The new raw data type is defined in agilent-raw-data-types.xml where the 1-channel type is defined analogously to the Agilent 2-channel type available in a pristine BASE server.

Installation and upgrade instructions are found in the 'INSTALL' file.

Getting started

The below recipe is a minimalistic route to import an Agilent experiment into BASE where many optional but important steps are skipped.

  1. Install this package as described by the instructions in the 'INSTALL' file.
  2. Import reporter annotations.
  3. Create array designs.
  4. Import raw data.
    • Upload raw data files to BASE.
    • Create raw bioassays corresponding to your raw data.
    • Create an experiment and associate the new raw bioassays to it.
    • Click the 'Import...' button in the experiment properties view. This will import all data in one single batch.

Share the array designs created to appropriate users, e.g, to an Agilent group or group Everyone with 'RU' privileges.

Copyright (C) 2010 Jari Häkkinen
This file is part of Illumina plug-in package for BASE.
Available at
BASE main site:
This 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 3 of the License, or (at your
option) any later version.
The software is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <>.

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