

@1064

13 years 
Jari Häkkinen 
Addresses #118. Calculate target with median instead of mean.



@1063

13 years 
Jari Häkkinen 
Add qQuantiler to autodetection list.



@1062

13 years 
Jari Häkkinen 
Addresses #118. Added support to use either mean or median in target …



@1060

13 years 
Martin Svensson 
Fixes #195 Normalizers should ask user for how to calculate averages



@1059

13 years 
Jari Häkkinen 
Use functionality already in yat.



@1058

13 years 
Jari Häkkinen 
The normalizer package now depends in PluginUtilites? version 0.1



@1055

13 years 
Jari Häkkinen 
Reverting previuos commit on configure.ac, still requiring 0.5.3



@1054

13 years 
Jari Häkkinen 
Cleaned up iterator usage in qQN.cc



@1053

13 years 
Jari Häkkinen 
Addresses #208. Fixing typos.



@1052

13 years 
Jari Häkkinen 
Fixes #208. Reverted changeset:1045 and added requirement on yat 0.5.3.



@1051

13 years 
Jari Häkkinen 
Updated documentation on QuantileNormalization?.



@1050

13 years 
Jari Häkkinen 
Addresses #118. Nonlogged input values are expected, geometric mean …



@1049

13 years 
Jari Häkkinen 
Addresses #206. Last commit destroyed nan fixing in changeset:1045 for …



@1047

13 years 
Jari Häkkinen 
Fixes #206. Missing values in reference now works. Each probe with no …



@1045

13 years 
Jari Häkkinen 
Missing values now works with the implemented fix to avoid a bug in …



@1044

13 years 
Jari Häkkinen 
Addresses #118 and #206. If no assay data is given use the average of …



@1043

13 years 
Jari Häkkinen 
Addresses #118 and #206. This code produces the same result as the …



@1042

13 years 
Jari Häkkinen 
Changed qqn package name.



@1041

13 years 
Jari Häkkinen 
Changed qqn package name.



@1039

13 years 
Jari Häkkinen 
Fixes #190. target c++ added.



@1037

13 years 
Jari Häkkinen 
Removed duplicated code block.



@1036

13 years 
Jari Häkkinen 
Fixes #197. Abort functionality implemented.



@1034

13 years 
Jari Häkkinen 
Peter says: Use proper classes



@1029

13 years 
Jari Häkkinen 
Joining Nicklas change to UTF8 frenzy.



@1023

13 years 
Jari Häkkinen 
Addresses #197. In anticipation of abort functionality the underlying …



@1020

13 years 
Jari Häkkinen 
Addresses #118 and fixes #187.



@1014

14 years 
Jari Häkkinen 
Fixes #191. Added standard options and also assay annotation data file …



@1009

14 years 
Jari Häkkinen 
Removed nonused configure options inherited from the WeNNI package.



@1008

14 years 
Jari Häkkinen 
Clarified where the recommended install directory is located.



@1007

14 years 
Jari Häkkinen 
metadata is split into reporter and assay metadata. Added flags to …



@1003

14 years 
Jari Häkkinen 
Added support to select assays ... but the select is not used yet.



@1000

14 years 
Jari Häkkinen 
storeResult interface change, some code moved to super class.



@998

14 years 
Jari Häkkinen 
Addresses #118 and #183. Moved export of data to an export method.



@993

14 years 
Jari Häkkinen 
Addresses #118. First version of working qQuantileNormalizer.



@989

14 years 
Jari Häkkinen 
Missing values from BASE are empty fields, need to define field …



@981

14 years 
Martin Svensson 
Changed requirements to version 2.9 of BASE both in documentation and …



@979

14 years 
Jari Häkkinen 
2.9 BASE core API required since changeset:975



@977

14 years 
Martin Svensson 
References #119 Corrected the calculation of relative rank between …



@975

14 years 
Martin Svensson 
References #119 Some changes in the calculationpart. The plugin runs …



@973

14 years 
Jari Häkkinen 
Addresses #118. Required yat version is 0.5 or later



@972

14 years 
Jari Häkkinen 
Addresses #118. Load of java wrapper works but manual install of …



@971

14 years 
Martin Svensson 
Added libraryfiles to the ignorelist



@967

14 years 
Martin Svensson 
References #119 The plugin is mostly ready for testing



@966

14 years 
Martin Svensson 
References #119 Part of the normalization algorithm is implemented



@965

14 years 
Jari Häkkinen 
Corrected flags summary output



@964

14 years 
Jari Häkkinen 
Added support to add qQN source to the normalizer package.



@963

14 years 
Jari Häkkinen 
Improved configure.ac and added option to disable check on required libs.



@962

14 years 
Jari Häkkinen 
Added missing include statement.



@961

14 years 
Jari Häkkinen 
Refs #118 and #161. PluginUtilities? download support. Added distclean …



@960

14 years 
Jari Häkkinen 
Refs #118. Changes suggested by the yat developer team.



@958

14 years 
Martin Svensson 
Fixes #177 Add information about how to upgrade the normalization package.



@956

14 years 
Jari Häkkinen 
Removed stray character in configure.ac



@955

14 years 
Jari Häkkinen 
Refs #118. Changes suggested by the yat developer team.



@954

14 years 
Jari Häkkinen 
Refs #118. Changes suggested by the yat developer team.



@953

14 years 
Jari Häkkinen 
Refs #118. Changes suggested by the yat developer team.



@952

14 years 
Jari Häkkinen 
Addresses #118. Added underlying C++ binary for the qQuantile.



@951

14 years 
Martin Svensson 
References #119 Added pluginclass. The plugin doesn't really do …



@950

14 years 
Martin Svensson 
References #119 Moved some method from the QuantileNormalization? …



@949

14 years 
Martin Svensson 
Fixes #176 Create release document



@948

14 years 
Martin Svensson 
Fixes #168 MD5 sum should be automatically generated for a package



@947

14 years 
Martin Svensson 
Fixes #166 (net.sf.basedb.normalizers) Automatic progression of …



@946

14 years 
Martin Svensson 
References #161 Set external jarfiles to be ignored



@945

14 years 
Martin Svensson 
Fixes #161 (net.sf.basedb.normalizers) Automatic download of BASE API



@934

14 years 
Jari Häkkinen 
Tagging version 1.0 of the net.sf.basedb.normalizers.



@933

14 years 
Jari Häkkinen 
Corrected spelling



@932

14 years 
Jari Häkkinen 
Addresses #120.



@931

14 years 
Jari Häkkinen 
Addresses #120. Preparing 1.0 release.



@930

14 years 
Jari Häkkinen 
Typo



@929

14 years 
Jari Häkkinen 
Removing CubicSplineNormalization? stub.



@928

14 years 
Jari Häkkinen 
Fixes #167. Now using geometric mean



@927

14 years 
Jari Häkkinen 
Refs #165.



@926

14 years 
Jari Häkkinen 
Fixes #165. Simply renamed rank invariant to quantile and made …



@925

14 years 
Jari Häkkinen 
Improved README.



@924

14 years 
Jari Häkkinen 



@923

14 years 
Martin Svensson 
References #163 Disregard the last commit. This will do instead.



@922

14 years 
Martin Svensson 
References #163 The sorting of spotdata should be stable now. Please …



@918

14 years 
Jari Häkkinen 
Removed stray lines.



@910

14 years 
Jari Häkkinen 
Changing normalizer package license to GPL3.



@909

14 years 
Jari Häkkinen 
Addresses #120.



@829

14 years 
Jari Häkkinen 
Setting svndigest:ignore on copies of trunks to avoid multiple counting.



@811

14 years 
Martin Svensson 
Fixes #141 Rank invariant should not support configurations. The …



@755

14 years 
Martin Svensson 
Fixed weaknesses discovered with FindBugs?eclipse plugin



@754

14 years 
Martin Svensson 
References #119 Change to only create a row summary array if it has …



@753

14 years 
Martin Svensson 
The SpotData2Ch objects are now compared by their ratiovalue and not …



@752

14 years 
Martin Svensson 
Fixes #119 Create Rank Invariant normalization



@751

14 years 
Martin Svensson 
References #119 Bugfixing



@750

14 years 
Martin Svensson 
References # 119 The normalization algorithm is almost done. Some …



@749

14 years 
Martin Svensson 
References # 119 Started with the development of this plugin. No …



@748

14 years 
Martin Svensson 
Fixes #117 Create average nomralization plugin.



@747

14 years 
Martin Svensson 
References #124 Corrected a few more copypaste mistake.



@746

14 years 
Martin Svensson 
Fixes #124 Corrected a copypaste mistake. Also added …



@745

14 years 
Martin Svensson 
References #117 Bugfixing



@744

14 years 
Martin Svensson 
References #117 Corrected a package name. Also changed the way global …



@743

14 years 
Martin Svensson 
References #117 The normalization is now done. Nothing has been tested …



@742

14 years 
Martin Svensson 
References #117 Cleaned up and refactored the classes. The Avg.norm. …



@740

14 years 
Martin Svensson 
Change name of the package


copied from plugins/base2/net.sf.basedb.normalizations:



@739

14 years 
Martin Svensson 
Added new files to the project such as license file, libraryfiles and …
