Timeline



May 19, 2009:

2:30 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) closed by Martin Svensson
fixed: (In [1087]) Fixes #195 net.sf.basedb.normalizers: Normalizers should …
2:30 PM Changeset [1087] by Martin Svensson
Fixes #195 net.sf.basedb.normalizers: Normalizers should ask user for …
2:25 PM net.sf.basedb.normalizers edited by Martin Svensson
(diff)
2:24 PM net.sf.basedb.normalizers edited by Martin Svensson
INSTALL and README links now points to the current stable version of … (diff)
11:43 AM Changeset [1086] by Nicklas Nordborg
References #212: Add support for exporting CGH data to MeV Fixed a …
9:46 AM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) closed by Nicklas Nordborg
fixed: (In [1085]) Fixes #215: BGX reporter importer hangs if the [Controls] …
9:46 AM Changeset [1085] by Nicklas Nordborg
Fixes #215: BGX reporter importer hangs if the [Controls] section has …

May 18, 2009:

2:59 PM Changeset [1084] by Martin Svensson
References #195 Updates everything except documentation/wiki, cause …
2:52 PM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) created by Jari Häkkinen
The BGX file for microRNA arrays is not exactly the same as for the …
2:51 PM Ticket #212 (Add support for exporting CGH data to MeV) closed by Nicklas Nordborg
fixed
2:19 PM Changeset [1083] by Nicklas Nordborg
References #212: Add support for exporting CGH data to MeV I have …
11:22 AM Changeset [1082] by Nicklas Nordborg
References #212: Add support for exporting CGH data to MeV The …
10:45 AM Changeset [1081] by Nicklas Nordborg
References #214: Move TDMS export to this extension Logged values can …

May 15, 2009:

7:48 PM Changeset [1080] by Jari Häkkinen
Changes for future release 0.3
7:38 PM Changeset [1079] by Jari Häkkinen
Fixes #118. qQuantiler will only show up in proper context and …
7:38 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) closed by Jari Häkkinen
fixed: (In [1079]) Fixes #118. qQuantiler will only show up in proper context …
7:34 PM PluginUtilities-0.2.tgz.MD5 attached to net.sf.basedb.pluginutilties by Jari Häkkinen
7:34 PM PluginUtilities-0.2.tgz attached to net.sf.basedb.pluginutilties by Jari Häkkinen
7:32 PM Changeset [1078] by Jari Häkkinen
Tagging version 0.2 of PluginUtilities?.
5:29 PM Changeset [1077] by Jari Häkkinen
Releasing version 0.2 of PluginUtilities?.
5:27 PM Changeset [1076] by Jari Häkkinen
Adding context checks for number of channels.
4:41 PM Changeset [1075] by Jari Häkkinen
Cleaner code, removed unused imports.
2:38 PM Changeset [1074] by Jari Häkkinen
Addresses #118. Added documentation for qQuantiler.
2:11 PM Changeset [1073] by Jari Häkkinen
Addresses #118. q=max(10,min(100,target_size/10))
1:28 PM Ticket #77 (Update information about webservice) closed by Nicklas Nordborg
fixed: Everything on that page was more than 18 months old. Even the …
1:26 PM Changeset [1072] by Jari Häkkinen
Fixing cut&paste typo. Thanks Peter.
1:13 PM net.sf.basedb.mev edited by Nicklas Nordborg
Added links to changelog to download table (diff)
11:53 AM Changeset [1071] by Nicklas Nordborg
References #214: Move TDMS export to this extension Removed …
11:06 AM Changeset [1070] by Nicklas Nordborg
Fixes #194: Default export file names should be more unique
11:06 AM Ticket #194 (Default export file names should be more unique) closed by Nicklas Nordborg
fixed: (In [1070]) Fixes #194: Default export file names should be more unique
11:03 AM Changeset [1069] by Nicklas Nordborg
References #214: Move TDMS export to this extension Removed some …
11:01 AM Changeset [1068] by Nicklas Nordborg
Fixes #214: Move TDMS export to this extension
11:01 AM Ticket #214 (Move TDMS export to this extension) closed by Nicklas Nordborg
fixed: (In [1068]) Fixes #214: Move TDMS export to this extension

May 14, 2009:

7:05 PM Changeset [1067] by Jari Häkkinen
Addresses #118. Forcing negative and 0 intensities to be NaNs? with 0 …
5:09 PM Changeset [1066] by Jari Häkkinen
Preparing for next milestone.
1:22 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) reopened by Martin Svensson
BASE 2.12 is required. Build.xml, base-plugins.xml and …
12:28 PM Changeset [1065] by Jari Häkkinen
Reverting changes commit by mistake to README.
12:26 PM Changeset [1064] by Jari Häkkinen
Addresses #118. Calculate target with median instead of mean.
12:01 PM Changeset [1063] by Jari Häkkinen
Add qQuantiler to autodetection list.
7:39 AM Ticket #207 (Illumina DASL arrays) closed by Jari Häkkinen
invalid

May 13, 2009:

8:09 AM Changeset [1062] by Jari Häkkinen
Addresses #118. Added support to use either mean or median in target …

May 11, 2009:

1:23 PM Changeset [1061] by Nicklas Nordborg
References #214: Move TDMS export to this extension The new exporter …
1:06 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) closed by Martin Svensson
fixed: (In [1060]) Fixes #195 Normalizers should ask user for how to …
1:06 PM Changeset [1060] by Martin Svensson
Fixes #195 Normalizers should ask user for how to calculate averages
12:36 PM Ticket #214 (Move TDMS export to this extension) created by Nicklas Nordborg
The BioAssaySetExporter is going through refactoring as described by …

May 8, 2009:

3:02 PM Changeset [1059] by Jari Häkkinen
Use functionality already in yat.
12:24 PM Changeset [1058] by Jari Häkkinen
The normalizer package now depends in PluginUtilites? version 0.1
12:18 PM PluginUtilities-0.1.tgz.MD5 attached to net.sf.basedb.pluginutilties by Jari Häkkinen
12:18 PM PluginUtilities-0.1.tgz attached to net.sf.basedb.pluginutilties by Jari Häkkinen
12:17 PM Changeset [1057] by Jari Häkkinen
Tagging version 0.1 of PluginUtilities?
12:15 PM Changeset [1056] by Jari Häkkinen
Preparing release 0.1 of PluginUtilities? package.

May 7, 2009:

12:43 AM Changeset [1055] by Jari Häkkinen
Reverting previuos commit on configure.ac, still requiring 0.5.3
12:41 AM Changeset [1054] by Jari Häkkinen
Cleaned up iterator usage in qQN.cc
12:30 AM Changeset [1053] by Jari Häkkinen
Addresses #208. Fixing typos.
12:28 AM Changeset [1052] by Jari Häkkinen
Fixes #208. Reverted changeset:1045 and added requirement on yat 0.5.3.
12:28 AM Ticket #208 (Revert changeset:1045 when yat bug ...) closed by Jari Häkkinen
fixed: (In [1052]) Fixes #208. Reverted changeset:1045 and added requirement …

May 6, 2009:

1:15 PM Changeset [1051] by Jari Häkkinen
Updated documentation on QuantileNormalization?.
11:11 AM Changeset [1050] by Jari Häkkinen
Addresses #118. Non-logged input values are expected, geometric mean …
9:20 AM Changeset [1049] by Jari Häkkinen
Addresses #206. Last commit destroyed nan fixing in changeset:1045 for …

May 4, 2009:

11:46 AM Changeset [1048] by Nicklas Nordborg
Fixes #213: Cannot save MeV options It was caused by #203 and never …
11:46 AM Ticket #213 (Cannot save MeV options) closed by Nicklas Nordborg
fixed: (In [1048]) Fixes #213: Cannot save MeV options It was caused by #203

Apr 30, 2009:

11:47 AM Ticket #213 (Cannot save MeV options) created by Nicklas Nordborg
It is not possible to save options for MeV. The options dialog is …

Apr 28, 2009:

8:12 AM Ticket #212 (Add support for exporting CGH data to MeV) created by Nicklas Nordborg
This is supposed to be straightforward the format is well-defined.

Apr 27, 2009:

4:24 PM Ticket #211 (Request: R/G quantile normalization) created by Jari Häkkinen
Copied from the BASE users mailing list (April 27, 2009): Yannick …
3:32 PM Ticket #210 (net.sf.basedb.normalizers: Add proper 2-channel support to ...) created by Jari Häkkinen
That is, keep our old favourite A \propto ln(ch1*ch2) the same value …
3:24 PM Changeset [1047] by Jari Häkkinen
Fixes #206. Missing values in reference now works. Each probe with no …
3:24 PM Ticket #206 (net.sf.basedb.normalizers: Make qQuantileNormalization handle missing ...) closed by Jari Häkkinen
fixed: (In [1047]) Fixes #206. Missing values in reference now works. Each …
1:14 PM Changeset [1046] by Jari Häkkinen
Debugging should be turned if in repository code.
11:30 AM Ticket #209 (Export of data to data repositories such as GEO and ArrayExpress) created by Jari Häkkinen
We should create an export plug-in/extesion for the GEO repository, …

Apr 24, 2009:

10:54 PM Ticket #208 (Revert changeset:1045 when yat bug ...) created by Jari Häkkinen
Revert changeset:1045 when yat bug …
10:52 PM Changeset [1045] by Jari Häkkinen
Missing values now works with the implemented fix to avoid a bug in …
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