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plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails
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$Id: README_PluginDetails 1114 2009-06-09 22:09:36Z jari $
Introduction
There are many plug-ins in the Illumina plug-in package for BASE. This file gives detailed information on some of the contributed plug-ins.
Illumina detection P-value calculation
This plug-in implements BeadStudio like detection P-value calculations for Illumina expression data (see http://www.genomecenter.ucdavis.edu/expression_analysis/documents/illumina_normalization_081201.pdf) on detection P-values.
The plug-in will always base the detection P-value calculation on raw data values, i.e., the mean raw intensity for the different signals. However, only reporters included in the bioassay set will be included in the calculations. This means that if there are no negative control bead types are left in the bioassay set, there is no distribution of negative controls to base the P-value detection calculation on. Or, if there are too few negative controls the detection P-value calculation is unreliable. (There is a request, http://baseplugins.thep.lu.se/ticket/204, for an user selectable option to use all available negative controls available in raw data irrespective the probe filtering state of the bio assayset.)
Hence, always use the detection P-value plug-in before removing negative controls.
The detection P-value plug-in does not filter the assays, it provides the detection P-values usable in a filter step after running this plug-in.
Parameters
The plug-in requires input of array type since detection P-values depends on array type.
The user can also set a cut off parameter to exclude outliers within
the negative controls. The cutoff defines the acceptable negative
control signal range
median-MAD*cutoff < I < median+MAD*cutoff
where MAD is the median absolute deviation.
Implementation details
Each assay is treated separately, i.e., no samples are combined together.
Retrieve the raw expression value for all negative controls in the current bioassay set.
Whole genome beadchips:
For all signals i calculate the detection P-value as
Pvalue = 1-i/N where R is the rank of the signal i relative to the
negative controls and N is the number of negative controls.
Others (DASL, miRNA, VeraCode? DASL, and Focused Arrays):
For all signals i calculate the detection P-value as
Pvalue = 1/2 - erf( [i-AvgControl]/StdControl/sqrt(2) ) where
AvgControl is the average intensity of the negative controls,
StdControl is the standard deviation of the ... (to be defined and
implemented accordingly), and erf is the error function
(http://mathworld.wolfram.com/Erf.html). The error function is used
for arguments witin the range (-4,4). To save CPU cycles, the function
value for arguments outside this range is set to -1 and 1,
respectively.
Copyright (C) 2009 Jari Häkkinen This file is part of Illumina plug-in 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/>.
