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

Timestamp:

Jun 2, 2008, 12:32:02 PM (16 years ago)

Author:

markus

Comment:

--

se.lu.onk.IlluminaSNPNormalization

@@ -1 +1 @@
 = Illumina SNP Normalization =
 
-tQN is a strategy using quantile normalization to improve the quality of data from Illumina Infinium Whole-Genome Genotyping SNP Beadchips.
+tQN is a strategy using quantile normalization to improve the quality of data from Illumina Infinium Whole-Genome Genotyping SNP Beadchips described in
 
-The method will, together with normalized !HapMap data sets, be downloadable upon acceptance of the submitted manuscript describing tQN.
+''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 comments please send an email to johan.staaf@med.lu.se
+If you have suggestions, comments or bug reports, please send an email to johan.staaf@med.lu.se