|
|
|
@2176
|
10 years |
Jari Häkkinen |
Changes from release procedure and other minor things.
|
|
|
|
@2175
|
10 years |
Jari Häkkinen |
Added blank line in parameter help string
|
|
|
|
@2173
|
10 years |
Jari Häkkinen |
Refs #228 and #541. Improving doc and help string
|
|
|
|
@2167
|
10 years |
olle |
Refs #541. Rank invariant normalization updated to store data in same …
|
|
|
|
@2166
|
10 years |
olle |
Refs #228. Refs #541. Average normalization updated to untransform …
|
|
|
|
@2165
|
10 years |
olle |
Refs #228. Refs #541. Quantile normalization updated to untransform …
|
|
|
|
@2156
|
10 years |
olle |
Typo fixed in help text.
|
|
|
|
@2155
|
10 years |
Jari Häkkinen |
Minor improvements on help text
|
|
|
|
@2154
|
10 years |
olle |
Refs #228. Classes/files AverageNormalization.java and …
|
|
|
|
@1454
|
12 years |
Nicklas Nordborg |
Preparing 'Normalization package 1.1-beta' release.
|
|
|
|
@1410
|
12 years |
Nicklas Nordborg |
References #331: Updates required for BASE 3 support
The code …
|
|
|
|
@1295
|
13 years |
Nicklas Nordborg |
Fixes #280: Plug-in should suggest better job names
|
|
|
|
@1224
|
13 years |
Jari Häkkinen |
Reverting changset:1164.
|
|
|
|
@1220
|
13 years |
Jari Häkkinen |
Write error messages to stderr
|
|
|
|
@1185
|
14 years |
Jari Häkkinen |
Improved documentation.
|
|
|
|
@1177
|
14 years |
Jari Häkkinen |
Improved qQuantiler docs.
|
|
|
|
@1164
|
14 years |
Jari Häkkinen |
Fixes #247. A work around for the erroneous export from exportPlainMatrix.
|
|
|
|
@1144
|
14 years |
Martin Svensson |
References #228 Updated the method that calculates bioassayset's …
|
|
|
|
@1143
|
14 years |
Martin Svensson |
References #228 Added parameter to define which average method to use …
|
|
|
|
@1084
|
14 years |
Martin Svensson |
References #195 Updates everything except documentation/wiki, cause …
|
|
|
|
@1079
|
14 years |
Jari Häkkinen |
Fixes #118. qQuantiler will only show up in proper context and …
|
|
|
|
@1075
|
14 years |
Jari Häkkinen |
Cleaner code, removed unused imports.
|
|
|
|
@1074
|
14 years |
Jari Häkkinen |
Addresses #118. Added documentation for qQuantiler.
|
|
|
|
@1073
|
14 years |
Jari Häkkinen |
Addresses #118. q=max(10,min(100,target_size/10))
|
|
|
|
@1072
|
14 years |
Jari Häkkinen |
Fixing cut&paste typo. Thanks Peter.
|
|
|
|
@1067
|
14 years |
Jari Häkkinen |
Addresses #118. Forcing negative and 0 intensities to be NaNs? with 0 …
|
|
|
|
@1064
|
14 years |
Jari Häkkinen |
Addresses #118. Calculate target with median instead of mean.
|
|
|
|
@1062
|
14 years |
Jari Häkkinen |
Addresses #118. Added support to use either mean or median in target …
|
|
|
|
@1060
|
14 years |
Martin Svensson |
Fixes #195 Normalizers should ask user for how to calculate averages
|
|
|
|
@1059
|
14 years |
Jari Häkkinen |
Use functionality already in yat.
|
|
|
|
@1055
|
14 years |
Jari Häkkinen |
Reverting previuos commit on configure.ac, still requiring 0.5.3
|
|
|
|
@1054
|
14 years |
Jari Häkkinen |
Cleaned up iterator usage in qQN.cc
|
|
|
|
@1053
|
14 years |
Jari Häkkinen |
Addresses #208. Fixing typos.
|
|
|
|
@1052
|
14 years |
Jari Häkkinen |
Fixes #208. Reverted changeset:1045 and added requirement on yat 0.5.3.
|
|
|
|
@1051
|
14 years |
Jari Häkkinen |
Updated documentation on QuantileNormalization?.
|
|
|
|
@1050
|
14 years |
Jari Häkkinen |
Addresses #118. Non-logged input values are expected, geometric mean …
|
|
|
|
@1049
|
14 years |
Jari Häkkinen |
Addresses #206. Last commit destroyed nan fixing in changeset:1045 for …
|
|
|
|
@1047
|
14 years |
Jari Häkkinen |
Fixes #206. Missing values in reference now works. Each probe with no …
|
|
|
|
@1045
|
14 years |
Jari Häkkinen |
Missing values now works with the implemented fix to avoid a bug in …
|
|
|
|
@1044
|
14 years |
Jari Häkkinen |
Addresses #118 and #206. If no assay data is given use the average of …
|
|
|
|
@1043
|
14 years |
Jari Häkkinen |
Addresses #118 and #206. This code produces the same result as the …
|
|
|
|
@1041
|
14 years |
Jari Häkkinen |
Changed qqn package name.
|
|
|
|
@1037
|
14 years |
Jari Häkkinen |
Removed duplicated code block.
|
|
|
|
@1036
|
14 years |
Jari Häkkinen |
Fixes #197. Abort functionality implemented.
|
|
|
|
@1034
|
14 years |
Jari Häkkinen |
Peter says: Use proper classes
|
|
|
|
@1023
|
14 years |
Jari Häkkinen |
Addresses #197. In anticipation of abort functionality the underlying …
|
|
|
|
@1020
|
15 years |
Jari Häkkinen |
Addresses #118 and fixes #187.
|
|
|
|
@1014
|
15 years |
Jari Häkkinen |
Fixes #191. Added standard options and also assay annotation data file …
|
|
|
|
@1009
|
15 years |
Jari Häkkinen |
Removed non-used configure options inherited from the WeNNI package.
|
|
|
|
@1007
|
15 years |
Jari Häkkinen |
metadata is split into reporter and assay metadata. Added flags to …
|
|
|
|
@1003
|
15 years |
Jari Häkkinen |
Added support to select assays ... but the select is not used yet.
|
|
|
|
@1000
|
15 years |
Jari Häkkinen |
storeResult interface change, some code moved to super class.
|
|
|
|
@998
|
15 years |
Jari Häkkinen |
Addresses #118 and #183. Moved export of data to an export method.
|
|
|
|
@993
|
15 years |
Jari Häkkinen |
Addresses #118. First version of working qQuantileNormalizer.
|
|
|
|
@989
|
15 years |
Jari Häkkinen |
Missing values from BASE are empty fields, need to define field …
|
|
|
|
@977
|
15 years |
Martin Svensson |
References #119 Corrected the calculation of relative rank between …
|
|
|
|
@975
|
15 years |
Martin Svensson |
References #119 Some changes in the calculation-part. The plug-in runs …
|
|
|
|
@973
|
15 years |
Jari Häkkinen |
Addresses #118. Required yat version is 0.5 or later
|
|
|
|
@967
|
15 years |
Martin Svensson |
References #119 The plug-in is mostly ready for testing
|
|
|
|
@966
|
15 years |
Martin Svensson |
References #119 Part of the normalization algorithm is implemented
|
|
|
|
@965
|
15 years |
Jari Häkkinen |
Corrected flags summary output
|
|
|
|
@964
|
15 years |
Jari Häkkinen |
Added support to add qQN source to the normalizer package.
|
|
|
|
@963
|
15 years |
Jari Häkkinen |
Improved configure.ac and added option to disable check on required libs.
|
|
|
|
@962
|
15 years |
Jari Häkkinen |
Added missing include statement.
|
|
|
|
@960
|
15 years |
Jari Häkkinen |
Refs #118. Changes suggested by the yat developer team.
|
|
|
|
@956
|
15 years |
Jari Häkkinen |
Removed stray character in configure.ac
|
|
|
|
@955
|
15 years |
Jari Häkkinen |
Refs #118. Changes suggested by the yat developer team.
|
|
|
|
@954
|
15 years |
Jari Häkkinen |
Refs #118. Changes suggested by the yat developer team.
|
|
|
|
@953
|
15 years |
Jari Häkkinen |
Refs #118. Changes suggested by the yat developer team.
|
|
|
|
@952
|
15 years |
Jari Häkkinen |
Addresses #118. Added underlying C++ binary for the qQuantile.
|
|
|
|
@951
|
15 years |
Martin Svensson |
References #119 Added plugin-class. The plugin doesn't really do …
|
|
|
|
@950
|
15 years |
Martin Svensson |
References #119 Moved some method from the QuantileNormalization? …
|
|
|
|
@947
|
15 years |
Martin Svensson |
Fixes #166 (net.sf.basedb.normalizers) Automatic progression of …
|
|
|
|
@931
|
15 years |
Jari Häkkinen |
Addresses #120. Preparing 1.0 release.
|
|
|
|
@930
|
15 years |
Jari Häkkinen |
Typo
|
|
|
|
@929
|
15 years |
Jari Häkkinen |
Removing CubicSplineNormalization? stub.
|
|
|
|
@928
|
15 years |
Jari Häkkinen |
Fixes #167. Now using geometric mean
|
|
|
|
@927
|
15 years |
Jari Häkkinen |
Refs #165.
|
|
|
|
@926
|
15 years |
Jari Häkkinen |
Fixes #165. Simply renamed rank invariant to quantile and made …
|
|
|
|
@924
|
15 years |
Jari Häkkinen |
|
|
|
|
@923
|
15 years |
Martin Svensson |
References #163 Disregard the last commit. This will do instead.
|
|
|
|
@922
|
15 years |
Martin Svensson |
References #163 The sorting of spotdata should be stable now. Please …
|
|
|
|
@910
|
15 years |
Jari Häkkinen |
Changing normalizer package license to GPL3.
|
|
|
|
@909
|
15 years |
Jari Häkkinen |
Addresses #120.
|
|
|
|
@811
|
15 years |
Martin Svensson |
Fixes #141 Rank invariant should not support configurations. The …
|
|
|
|
@755
|
15 years |
Martin Svensson |
Fixed weaknesses discovered with FindBugs?-eclipse plug-in
|
|
|
|
@754
|
15 years |
Martin Svensson |
References #119 Change to only create a row summary array if it has …
|
|
|
|
@753
|
15 years |
Martin Svensson |
The SpotData2Ch objects are now compared by their ratio-value and not …
|
|
|
|
@752
|
15 years |
Martin Svensson |
Fixes #119 Create Rank Invariant normalization
|
|
|
|
@751
|
15 years |
Martin Svensson |
References #119 Bug-fixing
|
|
|
|
@750
|
15 years |
Martin Svensson |
References # 119 The normalization algorithm is almost done. Some …
|
|
|
|
@749
|
15 years |
Martin Svensson |
References # 119 Started with the development of this plug-in. No …
|
|
|
|
@748
|
15 years |
Martin Svensson |
Fixes #117 Create average nomralization plug-in.
|
|
|
|
@746
|
15 years |
Martin Svensson |
Fixes #124 Corrected a copy-paste mistake. Also added …
|
|
|
|
@745
|
15 years |
Martin Svensson |
References #117 Bug-fixing
|
|
|
|
@744
|
15 years |
Martin Svensson |
References #117 Corrected a package name. Also changed the way global …
|
|
|
|
@743
|
15 years |
Martin Svensson |
References #117 The normalization is now done. Nothing has been tested …
|
|
|
|
@742
|
15 years |
Martin Svensson |
References #117 Cleaned up and refactored the classes. The Avg.norm. …
|
|
|
|
@740
|
15 years |
Martin Svensson |
Change name of the package
|
|
copied from plugins/base2/net.sf.basedb.normalizations/trunk/src:
|
|
|
|
@730
|
15 years |
Martin Svensson |
References #117 Average normalization plug-in is almost done. The …
|
