Timeline



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 …

Apr 23, 2009:

7:09 PM Changeset [1044] by Jari Häkkinen
Addresses #118 and #206. If no assay data is given use the average of …
6:55 PM Changeset [1043] by Jari Häkkinen
Addresses #118 and #206. This code produces the same result as the …
6:31 PM uk.ac.ebi.Tab2MageExporter edited by Jari Häkkinen
Fixed broken links. (diff)
10:11 AM Ticket #207 (Illumina DASL arrays) created by Jari Häkkinen
Make sure that DASL arrays can be used in BASE. Detection p-value …

Apr 20, 2009:

10:41 PM Changeset [1042] by Jari Häkkinen
Changed qqn package name.
10:37 PM Changeset [1041] by Jari Häkkinen
Changed qqn package name.
9:56 PM Ticket #206 (net.sf.basedb.normalizers: Make qQuantileNormalization handle missing ...) created by Jari Häkkinen
9:44 PM Changeset [1040] by Jari Häkkinen
Use getCurrentBioAssaySet in configuration phase.

Apr 16, 2009:

11:59 AM Ticket #190 (net.sf.basedb.normalizers: Add target that tries to build qQN if requested) closed by Jari Häkkinen
fixed: (In [1039]) Fixes #190. target c++ added.
11:59 AM Changeset [1039] by Jari Häkkinen
Fixes #190. target c++ added.

Apr 14, 2009:

3:56 PM Ticket #205 (Change link README_PluginDetails to point to tags at next release) created by Jari Häkkinen
The information in …
3:53 PM net.sf.basedb.illumina edited by Jari Häkkinen
Added link to detail information of the detection P-value plug-in. (diff)
3:47 PM Changeset [1038] by Jari Häkkinen
Added some detailed information on detection P-calue plug-in
3:42 PM Ticket #204 (Add option to include all available negative controls in detection ...) created by Jari Häkkinen
Add an user selectable option to use all in raw data available …

Apr 8, 2009:

5:23 PM Changeset [1037] by Jari Häkkinen
Removed duplicated code block.
12:07 AM Changeset [1036] by Jari Häkkinen
Fixes #197. Abort functionality implemented.
12:07 AM Ticket #197 (net.sf.basedb.normalizers: Add abort functionaly to qQuantileNormalizers) closed by Jari Häkkinen
fixed: (In [1036]) Fixes #197. Abort functionality implemented.
12:06 AM Changeset [1035] by Jari Häkkinen
Addresses #197. Abort functionality in place in abstract class.

Apr 7, 2009:

11:22 PM Changeset [1034] by Jari Häkkinen
Peter says: Use proper classes
8:27 AM Changeset [1033] by Nicklas Nordborg
Fixes #200: Change source files to UTF-8
8:27 AM Ticket #200 (Change source files to UTF-8) closed by Nicklas Nordborg
fixed: (In [1033]) Fixes #200: Change source files to UTF-8
8:24 AM Changeset [1032] by Nicklas Nordborg
Fixes #202: Change source files to UTF-8
8:24 AM Ticket #202 (Change source files to UTF-8) closed by Nicklas Nordborg
fixed: (In [1032]) Fixes #202: Change source files to UTF-8
8:15 AM Changeset [1031] by Jari Häkkinen
Joining Nicklas change to UTF-8 frenzy.
8:14 AM Changeset [1030] by Nicklas Nordborg
Fixes #199: Change source files to UTF-8
8:14 AM Ticket #199 (Change source files to UTF-8) closed by Nicklas Nordborg
fixed: (In [1030]) Fixes #199: Change source files to UTF-8
8:14 AM Changeset [1029] by Jari Häkkinen
Joining Nicklas change to UTF-8 frenzy.
8:10 AM Changeset [1028] by Nicklas Nordborg
References #203: Change source files to UTF-8 Changed 'Hakkinen' to …
8:08 AM Changeset [1027] by Nicklas Nordborg
References #198: Change source files to UTF-8 It is safer to set …
8:06 AM Ticket #203 (Change source files to UTF-8) closed by Nicklas Nordborg
fixed: (In [1026]) Fixes #203: Change source files to UTF-8
8:06 AM Changeset [1026] by Nicklas Nordborg
Fixes #203: Change source files to UTF-8
7:59 AM Changeset [1025] by Nicklas Nordborg
Fixes #201: Change source files to UTF-8
7:59 AM Ticket #201 (Change source files to UTF-8) closed by Nicklas Nordborg
fixed: (In [1025]) Fixes #201: Change source files to UTF-8
7:56 AM Ticket #198 (Change source files to UTF-8) closed by Nicklas Nordborg
fixed: (In [1024]) Fixes #198: Change source files to UTF-8
7:56 AM Changeset [1024] by Nicklas Nordborg
Fixes #198: Change source files to UTF-8
12:35 AM Changeset [1023] by Jari Häkkinen
Addresses #197. In anticipation of abort functionality the underlying …

Apr 6, 2009:

7:16 PM Ticket #184 (qQuantileNormalizer should update progress bar) closed by Jari Häkkinen
fixed: (In [1022]) Fixes #184. Progress bar is updated in the abstract class only.
7:16 PM Changeset [1022] by Jari Häkkinen
Fixes #184. Progress bar is updated in the abstract class only.
2:56 PM Ticket #203 (Change source files to UTF-8) created by Nicklas Nordborg
See http://base.thep.lu.se/ticket/1290
2:56 PM Ticket #202 (Change source files to UTF-8) created by Nicklas Nordborg
See http://base.thep.lu.se/ticket/1290
2:56 PM Ticket #201 (Change source files to UTF-8) created by Nicklas Nordborg
See http://base.thep.lu.se/ticket/1290
2:55 PM Ticket #200 (Change source files to UTF-8) created by Nicklas Nordborg
See http://base.thep.lu.se/ticket/1290
2:55 PM Ticket #199 (Change source files to UTF-8) created by Nicklas Nordborg
See http://base.thep.lu.se/ticket/1290
2:55 PM Ticket #198 (Change source files to UTF-8) created by Nicklas Nordborg
See http://base.thep.lu.se/ticket/1290
9:59 AM Ticket #189 (Add toolbar extension examples) closed by Nicklas Nordborg
fixed: (In [1021]) Fixes #189: Add toolbar extension examples
9:59 AM Changeset [1021] by Nicklas Nordborg
Fixes #189: Add toolbar extension examples

Apr 3, 2009:

11:55 AM Ticket #197 (net.sf.basedb.normalizers: Add abort functionaly to qQuantileNormalizers) created by Jari Häkkinen
The underlying abstract plug-in class must be changed as well.
11:53 AM Changeset [1020] by Jari Häkkinen
Addresses #118 and fixes #187.
11:53 AM Ticket #187 (qQuantileNormalizer should allow user to select the normaliztion ...) closed by Jari Häkkinen
fixed: (In [1020]) Addresses #118 and fixes #187.
11:41 AM Ticket #196 (Illumina methylation arrays ...) created by Jari Häkkinen
Illumina methylation arrays are 2-channel data (like Illumina SNP …
10:38 AM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) created by Jari Häkkinen
The Average Normalization plug-in always use the geometric mean but …
9:14 AM Changeset [1019] by Nicklas Nordborg
References #189: Add toolbar extension examples Added "Annotation …

Mar 31, 2009:

1:12 PM Ticket #194 (Default export file names should be more unique) created by Jari Häkkinen
I am using the brilliant MeV extension. BASE creates the TDMS file …
11:11 AM Changeset [1018] by Nicklas Nordborg
Changes for future release 1.3
11:09 AM Milestone MEV Launcher v1.2 completed
Bug fixes for MEV Launcher 1.1. See [wiki:net.sf.basedb.mev MEV …
11:09 AM net.sf.basedb.mev edited by Nicklas Nordborg
Releasing MeV Launcher 1.2 (diff)
11:06 AM mev-launcher-1.2.tar.gz attached to net.sf.basedb.mev by Nicklas Nordborg
MeV Launcher 1.2
11:05 AM Changeset [1017] by Nicklas Nordborg
Tagging MeV Launcher 1.2
11:04 AM Changeset [1016] by Nicklas Nordborg
Preparing release of MeV Launcher 1.2
10:57 AM Ticket #192 (MeV unable to launch appplication ... class not found exception) closed by Nicklas Nordborg
duplicate: Seems like this problem was fixed by #193.
9:03 AM Changeset [1015] by Nicklas Nordborg
Fixes #193: Use one JNLP file for each pre-signed JAR file
9:03 AM Ticket #193 (Use one JNLP file for each pre-signed JAR file) closed by Nicklas Nordborg
fixed: (In [1015]) Fixes #193: Use one JNLP file for each pre-signed JAR file
8:08 AM Ticket #193 (Use one JNLP file for each pre-signed JAR file) created by Nicklas Nordborg
According to the JNLP specification all JAR:s that are referenced in a …

Mar 30, 2009:

6:40 PM Changeset [1014] by Jari Häkkinen
Fixes #191. Added standard options and also assay annotation data file …
6:40 PM Ticket #191 (net.sf.basedb.normalizers: qQN should support standard options ...) closed by Jari Häkkinen
fixed: (In [1014]) Fixes #191. Added standard options and also assay …
3:24 PM Ticket #192 (MeV unable to launch appplication ... class not found exception) created by Jari Häkkinen
I cannot launch MeV with the BASE 2.11.0. I have pasted the stack …
10:48 AM PluginDownload edited by Nicklas Nordborg
(diff)
10:47 AM Changeset [1013] by Nicklas Nordborg
Preparing for future release 1.2
10:46 AM Milestone MEV Launcher v1.1 completed
This release of the MEV Launcher is focused on upgrading to MeV 4.3. …
10:45 AM Ticket #162 (Upgrade to MeV 4.3) closed by Nicklas Nordborg
fixed
10:45 AM net.sf.basedb.mev edited by Nicklas Nordborg
Releasing MeV Launcher 1.1 (diff)
10:38 AM Changeset [1012] by Nicklas Nordborg
Tagging version 1.1
10:37 AM Changeset [1011] by Nicklas Nordborg
Preparing release 1.1
10:00 AM Changeset [1010] by Nicklas Nordborg
References #162: Upgrade to MeV 4.3 Fixes some problems when starting …
9:59 AM Ticket #191 (net.sf.basedb.normalizers: qQN should support standard options ...) created by Jari Häkkinen
--version and --help
9:57 AM Changeset [1009] by Jari Häkkinen
Removed non-used configure options inherited from the WeNNI package.
9:56 AM Ticket #190 (net.sf.basedb.normalizers: Add target that tries to build qQN if requested) created by Jari Häkkinen
Something like 'ant qQN' should try to create an qQN binary and place …
9:40 AM Ticket #186 (qQuantileNormalizer method storeResult must be reimplemented) closed by Jari Häkkinen
fixed: As of changeset:1000 storeResult takes a SpotBatcher that is used to …
8:31 AM Changeset [1008] by Jari Häkkinen
Clarified where the recommended install directory is located.
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