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$Id: README_PluginDetails 1168 20090929 09:53:15Z 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/illumina_normalization_081201.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 signals. By default the calculations are based on negative controls available in the root bioassay set for the current analysis branch. The user may change this to only use negative controls in the current bioassay set.
The detection Pvalue plugin does not filter the assays, it provides the detection Pvalues usable in a filter step after running this plugin.
Parameters
The plugin requires input of array type since detection Pvalue are calculated differently depending on array type.
Users may select to use negative controls in the current bioassay set only. The default behaviour is to use all negative controls in the root bioassay set for the current bioassay set.
A cut off parameter is available to exclude outliers within
the negative controls. The cutoff
defines the acceptable negative
control signal range
medianMAD*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. All calculations are made on the raw beadtype level data, i.e., on the average expression value for each bead type and raw data is always used irrespective when in analysis the detection Pvalue is calculated.
Pvalue calculation for whole genome arrays:
For all signals i
calculate the detection Pvalue as
Pvalue = 1R/N
where R
is the rank of the signal i
relative to the
negative controls and N
is the number of negative controls.
Pvalue calculation for others array types (DASL, miRNA, VeraCode DASL, and Focused Arrays):
For all signals i
calculate the detection Pvalue as
Pvalue = 1/2  1/2 * erf( [iAvgControl]/StdControl/sqrt(2) )
where
AvgControl
is the average intensity of the negative controls,
StdControl
is the standard deviation of the the negative controls,
and erf
is the error function
(http://mathworld.wolfram.com/Erf.html). The error function is used
for arguments within 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 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/>.