= 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'' [[BR]] 
J. Staaf, J. Vallon-Christersson, D. Lindgren, G. Juliusson, R. Rosenquist, M. Höglund, Å. Borg, M. Ringnér [[BR]] 
''submitted'' [[BR]]

=== License ===
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 [http://www.gnu.org/copyleft/gpl.html GNU General Public License].

=== Download tQN ===

=== How to use tQN ===

''Requirements''
  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''

=== Contact ===

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