source:
plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails
@
1114
Last change on this file since 1114 was 1114, checked in by , 14 years ago  



File size: 3.6 KB 
$Id: README_PluginDetails 1114 20090609 22:09:36Z 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. 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 Pvalue detection calculation on. Or, if there are too few negative controls the detection Pvalue 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 Pvalue plugin before removing negative controls.
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 Pvalues 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
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.
Retrieve the raw expression value for all negative controls in the current bioassay set.
Whole genome beadchips:
For all signals i
calculate the detection Pvalue as
Pvalue = 1i/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 Pvalue as
Pvalue = 1/2  erf( [iAvgControl]/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 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/>.