Changes between Version 2 and Version 3 of se.lu.onk.IlluminaSNPNormalization


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Timestamp:
Jun 2, 2008, 12:32:02 PM (13 years ago)
Author:
markus
Comment:

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  • se.lu.onk.IlluminaSNPNormalization

    v2 v3  
    11= Illumina SNP Normalization =
    22
    3 tQN is a strategy using quantile normalization to improve the quality of data from Illumina Infinium Whole-Genome Genotyping SNP Beadchips.
     3tQN is a strategy using quantile normalization to improve the quality of data from Illumina Infinium Whole-Genome Genotyping SNP Beadchips described in
    44
    5 The method will, together with normalized !HapMap data sets, be downloadable upon acceptance of the submitted manuscript describing tQN.
     5''Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios'' [[BR]]
     6J. Staaf, J. Vallon-Christersson, D. Lindgren, G. Juliusson, R. Rosenquist, M. Höglund, Å. Borg, M. Ringnér [[BR]]
     7''submitted'' [[BR]]
     8
     9=== License ===
     10The tQN software is available as a stand-alone software package, and will become available as
     11as 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].
     12
     13=== Download tQN ===
     14
     15=== How to use tQN ===
     16
     17''Requirements''
     18  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.
     19
     20''Input data format''
     21  tQN is applied to data exported from !BeadStudio.
     22
     23''Running the program''
    624
    725=== Contact ===
    826
    9 If you have comments please send an email to johan.staaf@med.lu.se
     27If you have suggestions, comments or bug reports, please send an email to johan.staaf@med.lu.se