source: plugins/base2

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Diff Rev Age Author Log Message
(edit) @1164   14 years Jari Häkkinen Fixes #247. A work around for the erroneous export from exportPlainMatrix.
(edit) @1149   14 years Nicklas Nordborg Fixes #240: Bead summary importer should have an option to fail if the …
(edit) @1148   14 years Nicklas Nordborg Fixes #238: Supply plug-in configuration files for MicroRNA files
(edit) @1147   14 years Nicklas Nordborg Fixes #237: Add support for MicroRNA BGX files to reporter importer
(edit) @1146   14 years Nicklas Nordborg Fixes #239: BGX reporter/feature importer auto-detection matches any …
(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) @1142   14 years Martin Svensson Fixes #180 Overview plot extensions for Illumina expression
(edit) @1141   14 years Martin Svensson References #180 The work with the plotting extension is now finished …
(edit) @1137   14 years Martin Svensson References #180. Some necassary libraries for the JFreePlots.
(edit) @1136   14 years Martin Svensson References #180. Some necassary libraries for the JFreePlots.
(edit) @1135   14 years Martin Svensson References #180 The overview plots are almost finished. Some smaller …
(edit) @1133   14 years Martin Svensson References #180 Created classes for the control summary plots.
(edit) @1124   14 years Jari Häkkinen Fixes #231.
(edit) @1123   14 years Jari Häkkinen Fixed CamelCase escape
(edit) @1122   14 years Jari Häkkinen Fixes #227.
(edit) @1121   14 years Jari Häkkinen Fixes #230. Lower limit is now 1.
(edit) @1120   14 years Jari Häkkinen Fixes #232.
(edit) @1114   14 years Jari Häkkinen Addresses #113. The Pvalue calculation is in place. Need to figure …
(edit) @1113   14 years Jari Häkkinen Addresses #227
(edit) @1112   14 years Jari Häkkinen Addresses #227
(edit) @1111   14 years Jari Häkkinen Adding and changing svn properties.
(edit) @1097   14 years Martin Svensson References #180. The plot-extension is almost done. How the spot data …
(edit) @1093   14 years Martin Svensson References #182 The information is now inserted in the README file, in …
(edit) @1087   14 years Martin Svensson Fixes #195 net.sf.basedb.normalizers: Normalizers should ask user for …
(edit) @1085   14 years Nicklas Nordborg Fixes #215: BGX reporter importer hangs if the [Controls] section has …
(edit) @1084   14 years Martin Svensson References #195 Updates everything except documentation/wiki, cause …
(edit) @1080   14 years Jari Häkkinen Changes for future release 0.3
(edit) @1079   14 years Jari Häkkinen Fixes #118. qQuantiler will only show up in proper context and …
(edit) @1078   14 years Jari Häkkinen Tagging version 0.2 of PluginUtilities?.
(edit) @1077   14 years Jari Häkkinen Releasing version 0.2 of PluginUtilities?.
(edit) @1076   14 years Jari Häkkinen Adding context checks for number of channels.
(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) @1066   14 years Jari Häkkinen Preparing for next milestone.
(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) @1057   14 years Jari Häkkinen Tagging version 0.1 of PluginUtilities?
(edit) @1056   14 years Jari Häkkinen Preparing release 0.1 of PluginUtilities? package.
(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) @1046   14 years Jari Häkkinen Debugging should be turned if in repository code.
(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) @1040   14 years Jari Häkkinen Use getCurrentBioAssaySet in configuration phase.
(edit) @1039   14 years Jari Häkkinen Fixes #190. target c++ added.
(edit) @1038   14 years Jari Häkkinen Added some detailed information on detection P-calue plug-in
(edit) @1037   14 years Jari Häkkinen Removed duplicated code block.
(edit) @1036   14 years Jari Häkkinen Fixes #197. Abort functionality implemented.
(edit) @1035   14 years Jari Häkkinen Addresses #197. Abort functionality in place in abstract class.
(edit) @1034   14 years Jari Häkkinen Peter says: Use proper classes
(edit) @1032   14 years Nicklas Nordborg Fixes #202: Change source files to UTF-8
(edit) @1031   14 years Jari Häkkinen Joining Nicklas change to UTF-8 frenzy.
(edit) @1030   14 years Nicklas Nordborg Fixes #199: Change source files to UTF-8
(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) @1022   14 years Jari Häkkinen Fixes #184. Progress bar is updated in the abstract class only.
(edit) @1020   14 years Jari Häkkinen Addresses #118 and fixes #187.
(edit) @1014   15 years Jari Häkkinen Fixes #191. Added standard options and also assay annotation data file …
(edit) @1009   15 years Jari Häkkinen Removed non-used configure options inherited from the WeNNI package.
(edit) @1008   15 years Jari Häkkinen Clarified where the recommended install directory is located.
(edit) @1007   15 years Jari Häkkinen metadata is split into reporter and assay metadata. Added flags to …
(edit) @1006   15 years Jari Häkkinen metadata is split into reporter and assay metadata.
(edit) @1005   15 years Jari Häkkinen storeValues typo! Plural importantsvn diff
(edit) @1004   15 years Jari Häkkinen Removed warning suppressions, clean up of code, added missing …
(edit) @1003   15 years Jari Häkkinen Added support to select assays ... but the select is not used yet.
(edit) @1002   15 years Jari Häkkinen Added support to optionally select assays.
(edit) @1001   15 years Jari Häkkinen Minor changes to debug_option.
(edit) @1000   15 years Jari Häkkinen storeResult interface change, some code moved to super class.
(edit) @999   15 years Jari Häkkinen Restructured result storage.
(edit) @998   15 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) @992   15 years Jari Häkkinen Require BASE 2.5. Restructure build script.
(edit) @991   15 years Jari Häkkinen Minor things.
(edit) @990   15 years Jari Häkkinen Typo.
(edit) @989   15 years Jari Häkkinen Missing values from BASE are empty fields, need to define field …
(edit) @984   15 years Jari Häkkinen Added support to write to stdin of underlying binary ... added missing …
(edit) @983   15 years Jari Häkkinen Added support to write to stdin of underlying binary.
(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
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