source: plugins/base2/net.sf.basedb.illumina/trunk/README_PluginDetails @ 1114

Last change on this file since 1114 was 1114, checked in by Jari Häkkinen, 14 years ago

Addresses #113. The Pvalue calculation is in place. Need to figure details of std and average calculations.

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$Id: README_PluginDetails 1114 2009-06-09 22:09:36Z jari $


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 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,, 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.


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 ( 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
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
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 <>.

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