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

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Diff Rev Age Author Log Message
(edit) @2759   9 years Nicklas Nordborg References #652: New location of BASE JAR files Normalizers trunk.
(edit) @2284   10 years Nicklas Nordborg References #588: Update extensions to target Java 1.7 and BASE 3.3 …
(edit) @2182   10 years Nicklas Nordborg Fixes #552: PluginUtilities?-0.2.jar is in incorrect location Download …
(edit) @2181   10 years Nicklas Nordborg References #551: Add 'install' target to normalizers build script Add …
(edit) @2180   10 years Nicklas Nordborg Fixes #551: Add 'install' target to normalizers build script
(edit) @2179   10 years Nicklas Nordborg Update build path for Eclipse to use the BASE 3.2.4 jar files. Related …
(edit) @2176   10 years Jari Häkkinen Changes from release procedure and other minor things.
(edit) @2175   10 years Jari Häkkinen Added blank line in parameter help string
(edit) @2174   10 years olle Refs #541. Refs #228. Outermost Ant build XML file updated by …
(edit) @2173   10 years Jari Häkkinen Refs #228 and #541. Improving doc and help string
(edit) @2167   10 years olle Refs #541. Rank invariant normalization updated to store data in same …
(edit) @2166   10 years olle Refs #228. Refs #541. Average normalization updated to untransform …
(edit) @2165   10 years olle Refs #228. Refs #541. Quantile normalization updated to untransform …
(edit) @2156   10 years olle Typo fixed in help text.
(edit) @2155   10 years Jari Häkkinen Minor improvements on help text
(edit) @2154   10 years olle Refs #228. Classes/files AverageNormalization.java and …
(edit) @1454   12 years Nicklas Nordborg Preparing 'Normalization package 1.1-beta' release.
(edit) @1410   12 years Nicklas Nordborg References #331: Updates required for BASE 3 support The code …
(edit) @1295   13 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) @1219   13 years Jari Häkkinen Typo.
(edit) @1194   14 years Jari Häkkinen Typo.
(edit) @1186   14 years Jari Häkkinen Bumping BASE requirement to 2.15
(edit) @1185   14 years Jari Häkkinen Improved documentation.
(edit) @1177   14 years Jari Häkkinen Improved qQuantiler docs.
(edit) @1164   14 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) @1087   14 years Martin Svensson Fixes #195 net.sf.basedb.normalizers: Normalizers should ask user for …
(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) @1065   14 years Jari Häkkinen Reverting changes commit by mistake to README.
(edit) @1064   14 years Jari Häkkinen Addresses #118. Calculate target with median instead of mean.
(edit) @1063   14 years Jari Häkkinen Add qQuantiler to autodetection list.
(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) @1058   14 years Jari Häkkinen The normalizer package now depends in PluginUtilites? version 0.1
(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) @1042   14 years Jari Häkkinen Changed qqn package name.
(edit) @1041   14 years Jari Häkkinen Changed qqn package name.
(edit) @1039   14 years Jari Häkkinen Fixes #190. target c++ added.
(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) @1029   14 years Jari Häkkinen Joining Nicklas change to UTF-8 frenzy.
(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) @1008   14 years Jari Häkkinen Clarified where the recommended install directory is located.
(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   15 years Jari Häkkinen Addresses #118. First version of working qQuantileNormalizer.
(edit) @989   15 years Jari Häkkinen Missing values from BASE are empty fields, need to define field …
(edit) @981   15 years Martin Svensson Changed requirements to version 2.9 of BASE both in documentation and …
(edit) @979   15 years Jari Häkkinen 2.9 BASE core API required since changeset:975
(edit) @977   15 years Martin Svensson References #119 Corrected the calculation of relative rank between …
(edit) @975   15 years Martin Svensson References #119 Some changes in the calculation-part. The plug-in runs …
(edit) @973   15 years Jari Häkkinen Addresses #118. Required yat version is 0.5 or later
(edit) @972   15 years Jari Häkkinen Addresses #118. Load of java wrapper works but manual install of …
(edit) @971   15 years Martin Svensson Added library-files to the ignore-list
(edit) @967   15 years Martin Svensson References #119 The plug-in is mostly ready for testing
(edit) @966   15 years Martin Svensson References #119 Part of the normalization algorithm is implemented
(edit) @965   15 years Jari Häkkinen Corrected flags summary output
(edit) @964   15 years Jari Häkkinen Added support to add qQN source to the normalizer package.
(edit) @963   15 years Jari Häkkinen Improved configure.ac and added option to disable check on required libs.
(edit) @962   15 years Jari Häkkinen Added missing include statement.
(edit) @961   15 years Jari Häkkinen Refs #118 and #161. PluginUtilities? download support. Added distclean …
(edit) @960   15 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @958   15 years Martin Svensson Fixes #177 Add information about how to upgrade the normalization package.
(edit) @956   15 years Jari Häkkinen Removed stray character in configure.ac
(edit) @955   15 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @954   15 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @953   15 years Jari Häkkinen Refs #118. Changes suggested by the yat developer team.
(edit) @952   15 years Jari Häkkinen Addresses #118. Added underlying C++ binary for the qQuantile.
(edit) @951   15 years Martin Svensson References #119 Added plugin-class. The plugin doesn't really do …
(edit) @950   15 years Martin Svensson References #119 Moved some method from the QuantileNormalization? …
(edit) @949   15 years Martin Svensson Fixes #176 Create release document
(edit) @948   15 years Martin Svensson Fixes #168 MD5 sum should be automatically generated for a package
(edit) @947   15 years Martin Svensson Fixes #166 (net.sf.basedb.normalizers) Automatic progression of …
(edit) @946   15 years Martin Svensson References #161 Set external jar-files to be ignored
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