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plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails
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$Id: README_PluginDetails 1111 20090608 20:30:28Z jari $
Introduction
There are many plugins in the Illumina plugin package for BASE. This file gives detailed information on some of the contributed plugins.
Illumina detection Pvalue calculation
This plugin implements BeadStudio like detection Pvalue calculations for Illumina expression data (see http://www.genomecenter.ucdavis.edu/expression_analysis/documents/GEX__normalization_070313.pdf on detection Pvalues.
The plugin will always base the detection Pvalue calculation on raw data values, i.e., the mean raw intensity for the different bead types. However, only reporters included in the bioassay set will be included in the distributions. The effect of the reporter filtering that may have occurred is that if no negative control bead types are left in the bioassay set, there is no distribution of negative controls to base the Pvalue detection calculation on.
Hence, typically you should use the detection Pvalue plugin before you remove the negative controls from your analysis.
There is a request, http://baseplugins.thep.lu.se/ticket/204, for an user selectable option to use all available negative controls in raw data even if no negative controls are left in a bioassay set.
Copyright (C) 2009 Jari Häkkinen This file is part of Illumina plugin package for BASE. Available at http://baseplugins.thep.lu.se/ BASE main site: http://base.thep.lu.se/ 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 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 BASE. If not, see <http://www.gnu.org/licenses/>.