Version 3 (modified by markus, 16 years ago) ( diff )


Illumina SNP Normalization

tQN is a strategy using quantile normalization to improve the quality of data from Illumina Infinium Whole-Genome Genotyping SNP Beadchips described in

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios

  1. Staaf, J. Vallon-Christersson, D. Lindgren, G. Juliusson, R. Rosenquist, M. Höglund, Å. Borg, M. Ringnér



The tQN software is available as a stand-alone software package, and will become available as as a plug-in to BASE as the handling of SNP arrays in BASE is developed. Both versions under the GNU General Public License.

Download tQN

How to use tQN


tQN is written in R with a Perl wrapper. Required Perl modules are: File::Spec, Getopt::Long, IO::File and Pod::Usage. Required R package is limma.

Input data format

tQN is applied to data exported from BeadStudio.

Running the program


If you have suggestions, comments or bug reports, please send an email to johan.staaf@…

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