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

Last change on this file since 1215 was 1212, checked in by Jari Häkkinen, 14 years ago

Adding support to save background expression matrix to file.

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$Id: README_PluginDetails 1212 2010-03-26 11:02:17Z jari $


This file gives some details on some of the plug-ins in this package.

Background correction plug-in

This plug-in will remove a per-slide global background from all spots. The background is calculated from a set of negative control spot on the array. See implementation details below for details.


There is one parameter to set that specifies how background intensities should be calculated. Allowed values are median or mean, i.e. the background is either the median or the mean of the negative control spots on the array.

The expression of the background probes is optionally saved to a file. The default is not to save the expression matrix but this can be changed during job configuration.

Implementation details

Each assay is treated separately, i.e., no samples are combined together. All calculations are made on the current bioassay data implying that this plug-in should be used early in analysis and before background spots are removed.

A spot is considered to be a negative control spot if it has an External Id exactly matching the string (-)3xSLv1.

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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