source: plugins/base2/net.sf.basedb.normalizers/trunk/src

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Diff Rev Age Author Log Message
(edit) @1454   11 years Nicklas Nordborg Preparing 'Normalization package 1.1-beta' release.
(edit) @1410   11 years Nicklas Nordborg References #331: Updates required for BASE 3 support The code …
(edit) @1295   12 years Nicklas Nordborg Fixes #280: Plug-in should suggest better job names
(edit) @1224   13 years Jari Häkkinen Reverting changset:1164.
(edit) @1220   13 years Jari Häkkinen Write error messages to stderr
(edit) @1185   13 years Jari Häkkinen Improved documentation.
(edit) @1177   13 years Jari Häkkinen Improved qQuantiler docs.
(edit) @1164   13 years Jari Häkkinen Fixes #247. A work around for the erroneous export from exportPlainMatrix.
(edit) @1144   14 years Martin Svensson References #228 Updated the method that calculates bioassayset's …
(edit) @1143   14 years Martin Svensson References #228 Added parameter to define which average method to use …
(edit) @1084   14 years Martin Svensson References #195 Updates everything except documentation/wiki, cause …
(edit) @1079   14 years Jari Häkkinen Fixes #118. qQuantiler will only show up in proper context and …
(edit) @1075   14 years Jari Häkkinen Cleaner code, removed unused imports.
(edit) @1074   14 years Jari Häkkinen Addresses #118. Added documentation for qQuantiler.
(edit) @1073   14 years Jari Häkkinen Addresses #118. q=max(10,min(100,target_size/10))
(edit) @1072   14 years Jari Häkkinen Fixing cut&paste typo. Thanks Peter.
(edit) @1067   14 years Jari Häkkinen Addresses #118. Forcing negative and 0 intensities to be NaNs? with 0 …
(edit) @1064   14 years Jari Häkkinen Addresses #118. Calculate target with median instead of mean.
(edit) @1062   14 years Jari Häkkinen Addresses #118. Added support to use either mean or median in target …
(edit) @1060   14 years Martin Svensson Fixes #195 Normalizers should ask user for how to calculate averages
(edit) @1059   14 years Jari Häkkinen Use functionality already in yat.
(edit) @1055   14 years Jari Häkkinen Reverting previuos commit on configure.ac, still requiring 0.5.3
(edit) @1054   14 years Jari Häkkinen Cleaned up iterator usage in qQN.cc
(edit) @1053   14 years Jari Häkkinen Addresses #208. Fixing typos.
(edit) @1052   14 years Jari Häkkinen Fixes #208. Reverted changeset:1045 and added requirement on yat 0.5.3.
(edit) @1051   14 years Jari Häkkinen Updated documentation on QuantileNormalization?.
(edit) @1050   14 years Jari Häkkinen Addresses #118. Non-logged input values are expected, geometric mean …
(edit) @1049   14 years Jari Häkkinen Addresses #206. Last commit destroyed nan fixing in changeset:1045 for …
(edit) @1047   14 years Jari Häkkinen Fixes #206. Missing values in reference now works. Each probe with no …
(edit) @1045   14 years Jari Häkkinen Missing values now works with the implemented fix to avoid a bug in …
(edit) @1044   14 years Jari Häkkinen Addresses #118 and #206. If no assay data is given use the average of …
(edit) @1043   14 years Jari Häkkinen Addresses #118 and #206. This code produces the same result as the …
(edit) @1041   14 years Jari Häkkinen Changed qqn package name.
(edit) @1037   14 years Jari Häkkinen Removed duplicated code block.
(edit) @1036   14 years Jari Häkkinen Fixes #197. Abort functionality implemented.
(edit) @1034   14 years Jari Häkkinen Peter says: Use proper classes
(edit) @1023   14 years Jari Häkkinen Addresses #197. In anticipation of abort functionality the underlying …
(edit) @1020   14 years Jari Häkkinen Addresses #118 and fixes #187.
(edit) @1014   14 years Jari Häkkinen Fixes #191. Added standard options and also assay annotation data file …
(edit) @1009   14 years Jari Häkkinen Removed non-used configure options inherited from the WeNNI package.
(edit) @1007   14 years Jari Häkkinen metadata is split into reporter and assay metadata. Added flags to …
(edit) @1003   14 years Jari Häkkinen Added support to select assays ... but the select is not used yet.
(edit) @1000   14 years Jari Häkkinen storeResult interface change, some code moved to super class.
(edit) @998   14 years Jari Häkkinen Addresses #118 and #183. Moved export of data to an export method.
(edit) @993   14 years Jari Häkkinen Addresses #118. First version of working qQuantileNormalizer.
(edit) @989   14 years Jari Häkkinen Missing values from BASE are empty fields, need to define field …
(edit) @977   14 years Martin Svensson References #119 Corrected the calculation of relative rank between …
(edit) @975   14 years Martin Svensson References #119 Some changes in the calculation-part. The plug-in runs …
(edit) @973   14 years Jari Häkkinen Addresses #118. Required yat version is 0.5 or later
(edit) @967   14 years Martin Svensson References #119 The plug-in is mostly ready for testing
(edit) @966   14 years Martin Svensson References #119 Part of the normalization algorithm is implemented
(edit) @965   14 years Jari Häkkinen Corrected flags summary output
(edit) @964   14 years Jari Häkkinen Added support to add qQN source to the normalizer package.
(edit) @963   14 years Jari Häkkinen Improved configure.ac and added option to disable check on required libs.
(edit) @962   14 years Jari Häkkinen Added missing include statement.
(edit) @960   14 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @956   14 years Jari Häkkinen Removed stray character in configure.ac
(edit) @955   14 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @954   14 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @953   14 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @952   14 years Jari Häkkinen Addresses #118. Added underlying C++ binary for the qQuantile.
(edit) @951   14 years Martin Svensson References #119 Added plugin-class. The plugin doesn't really do …
(edit) @950   14 years Martin Svensson References #119 Moved some method from the QuantileNormalization?
(edit) @947   14 years Martin Svensson Fixes #166 (net.sf.basedb.normalizers) Automatic progression of …
(edit) @931   14 years Jari Häkkinen Addresses #120. Preparing 1.0 release.
(edit) @930   14 years Jari Häkkinen Typo
(edit) @929   14 years Jari Häkkinen Removing CubicSplineNormalization? stub.
(edit) @928   14 years Jari Häkkinen Fixes #167. Now using geometric mean
(edit) @927   14 years Jari Häkkinen Refs #165.
(edit) @926   14 years Jari Häkkinen Fixes #165. Simply renamed rank invariant to quantile and made …
(edit) @924   14 years Jari Häkkinen
(edit) @923   14 years Martin Svensson References #163 Disregard the last commit. This will do instead.
(edit) @922   14 years Martin Svensson References #163 The sorting of spotdata should be stable now. Please …
(edit) @910   14 years Jari Häkkinen Changing normalizer package license to GPL3.
(edit) @909   14 years Jari Häkkinen Addresses #120.
(edit) @811   14 years Martin Svensson Fixes #141 Rank invariant should not support configurations. The …
(edit) @755   14 years Martin Svensson Fixed weaknesses discovered with FindBugs?-eclipse plug-in
(edit) @754   14 years Martin Svensson References #119 Change to only create a row summary array if it has …
(edit) @753   14 years Martin Svensson The SpotData2Ch objects are now compared by their ratio-value and not …
(edit) @752   14 years Martin Svensson Fixes #119 Create Rank Invariant normalization
(edit) @751   14 years Martin Svensson References #119 Bug-fixing
(edit) @750   14 years Martin Svensson References # 119 The normalization algorithm is almost done. Some …
(edit) @749   14 years Martin Svensson References # 119 Started with the development of this plug-in. No …
(edit) @748   14 years Martin Svensson Fixes #117 Create average nomralization plug-in.
(edit) @746   14 years Martin Svensson Fixes #124 Corrected a copy-paste mistake. Also added …
(edit) @745   14 years Martin Svensson References #117 Bug-fixing
(edit) @744   14 years Martin Svensson References #117 Corrected a package name. Also changed the way global …
(edit) @743   14 years Martin Svensson References #117 The normalization is now done. Nothing has been tested …
(edit) @742   14 years Martin Svensson References #117 Cleaned up and refactored the classes. The Avg.norm. …
(copy) @740   14 years Martin Svensson Change name of the package
copied from plugins/base2/net.sf.basedb.normalizations/trunk/src:
(edit) @730   15 years Martin Svensson References #117 Average normalization plug-in is almost done. The …
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