Timeline
May 27, 2009:
- 4:20 PM PluginDownload edited by
- Removed non-working link. (diff)
- 4:14 PM PluginDownload edited by
- Added references to papers for some plug-ins (diff)
- 4:06 PM PluginDownload edited by
- (diff)
- 3:56 PM PluginDownload edited by
- Fixed BASE 1.2 plug-in list (diff)
- 2:37 PM PluginDownload edited by
- Restructured BASE 1.2 plug-in table list. (diff)
- 2:33 PM PluginDownload edited by
- Added link to WeNNI publication (diff)
- 2:16 PM Changeset [1093] by
- References #182 The information is now inserted in the README file, in …
- 2:16 PM Ticket #182 (Illumina probes not found message should be documented) updated by
- (In [1093]) References #182 The information is now inserted in the …
- 2:04 PM WikiStart edited by
- Made download link more visible. (diff)
- 11:09 AM Ticket #182 (Illumina probes not found message should be documented) updated by
-
Status, Owner changed
- 10:00 AM Changeset [1092] by
- References #217: GCT exporter Make sure assay names are unique in the …
- 10:00 AM Ticket #217 (GCT exporter) updated by
- (In [1092]) References #217: GCT exporter Make sure assay names are …
- 9:51 AM Changeset [1091] by
- Fixes #217: GCT exporter
- 9:51 AM Ticket #217 (GCT exporter) closed by
- fixed: (In [1091]) Fixes #217: GCT exporter
- 8:23 AM Ticket #217 (GCT exporter) updated by
-
Status changed
- 8:22 AM Ticket #216 (Setup source code repository for GenePattern integration) closed by
- fixed: (In [1090]) Fixes #216: Setup source code repository for GenePattern …
- 8:22 AM Changeset [1090] by
- Fixes #216: Setup source code repository for GenePattern integration
May 26, 2009:
- 12:55 PM Changeset [1089] by
- References #216: Setup source code repository for GenePattern …
- 12:55 PM Ticket #216 (Setup source code repository for GenePattern integration) updated by
- (In [1089]) References #216: Setup source code repository for …
- 12:53 PM Ticket #216 (Setup source code repository for GenePattern integration) updated by
-
Summary changed
- 12:53 PM Changeset [1088] by
- References #216: Setup source code repository for GenePattern integration
- 12:53 PM Ticket #216 (Setup source code repository for GenePattern integration) updated by
- (In [1088]) References #216: Setup source code repository for …
- 12:51 PM Ticket #216 (Setup source code repository for GenePattern integration) updated by
-
Status changed
- 12:50 PM Ticket #219 (Setup a GenePattern server for testing) created by
- I didn't manage to setup a server on my development machine. I got it …
- 12:46 PM Ticket #218 (Proof-of-concept: run a selected GenePattern module from BASE) created by
- It doesn't matter much which module that we choose, but it is …
- 11:14 AM Ticket #217 (GCT exporter) created by
- Create an exporter that can export a bioassay set to GCT format. This …
- 11:06 AM Ticket #216 (Setup source code repository for GenePattern integration) created by
- The usual standard directories, build.xml, readme, etc. that we need …
- 10:59 AM net.sf.basedb.genepattern edited by
- (diff)
- 10:57 AM net.sf.basedb.genepattern created by
- Created GenePattern wiki page
May 20, 2009:
- 1:08 PM Ticket #180 (Overview plot extensions for Illumina expression) updated by
-
Status, Owner, Milestone changed
May 19, 2009:
- 2:30 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) closed by
- fixed: (In [1087]) Fixes #195 net.sf.basedb.normalizers: Normalizers should …
- 2:30 PM Changeset [1087] by
- Fixes #195 net.sf.basedb.normalizers: Normalizers should ask user for …
- 2:25 PM net.sf.basedb.normalizers edited by
- (diff)
- 2:24 PM net.sf.basedb.normalizers edited by
- INSTALL and README links now points to the current stable version of … (diff)
- 11:43 AM Changeset [1086] by
- References #212: Add support for exporting CGH data to MeV Fixed a …
- 11:43 AM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- (In [1086]) References #212: Add support for exporting CGH data to MeV …
- 9:46 AM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) closed by
- fixed: (In [1085]) Fixes #215: BGX reporter importer hangs if the [Controls] …
- 9:46 AM Changeset [1085] by
- Fixes #215: BGX reporter importer hangs if the [Controls] section has …
- 9:12 AM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) updated by
-
Summary changed
- 9:08 AM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) updated by
-
Status changed
I know what is causing this. The problem is with the [Controls] …
May 18, 2009:
- 3:09 PM Ticket #215 (BGX reporter importer hangs if the [Controls] section has less than 6 ...) updated by
- On a freshly rebooted server I reach another status message with the …
- 2:59 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) updated by
- (In [1084]) References #195 Updates everything except …
- 2:59 PM Changeset [1084] by
- 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
- 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
- fixed
- 2:19 PM Changeset [1083] by
- References #212: Add support for exporting CGH data to MeV I have …
- 2:19 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- (In [1083]) References #212: Add support for exporting CGH data to MeV …
- 11:22 AM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- (In [1082]) References #212: Add support for exporting CGH data to MeV …
- 11:22 AM Changeset [1082] by
- References #212: Add support for exporting CGH data to MeV The …
- 10:45 AM Ticket #214 (Move TDMS export to this extension) updated by
- (In [1081]) References #214: Move TDMS export to this extension …
- 10:45 AM Changeset [1081] by
- References #214: Move TDMS export to this extension Logged values can …
May 15, 2009:
- 7:48 PM Changeset [1080] by
- Changes for future release 0.3
- 7:38 PM Changeset [1079] by
- 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
- fixed: (In [1079]) Fixes #118. qQuantiler will only show up in proper context …
- 7:32 PM Changeset [1078] by
- Tagging version 0.2 of PluginUtilities.
- 5:29 PM Changeset [1077] by
- Releasing version 0.2 of PluginUtilities.
- 5:27 PM Changeset [1076] by
- Adding context checks for number of channels.
- 4:41 PM Changeset [1075] by
- Cleaner code, removed unused imports.
- 2:38 PM Changeset [1074] by
- Addresses #118. Added documentation for qQuantiler.
- 2:38 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1074]) Addresses #118. Added documentation for qQuantiler.
- 2:14 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- It seems like the information in the documentation is incorrect. In …
- 2:11 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1073]) Addresses #118. q=max(10,min(100,target_size/10))
- 2:11 PM Changeset [1073] by
- Addresses #118. q=max(10,min(100,target_size/10))
- 1:28 PM Ticket #77 (Update information about webservice) closed by
- fixed: Everything on that page was more than 18 months old. Even the …
- 1:26 PM Changeset [1072] by
- Fixing cut&paste typo. Thanks Peter.
- 1:13 PM net.sf.basedb.mev edited by
- Added links to changelog to download table (diff)
- 11:53 AM Changeset [1071] by
- References #214: Move TDMS export to this extension Removed …
- 11:53 AM Ticket #214 (Move TDMS export to this extension) updated by
- (In [1071]) References #214: Move TDMS export to this extension …
- 11:06 AM Changeset [1070] by
- 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
- fixed: (In [1070]) Fixes #194: Default export file names should be more unique
- 11:05 AM Ticket #194 (Default export file names should be more unique) updated by
-
Status, Summary changed
- 11:03 AM Changeset [1069] by
- References #214: Move TDMS export to this extension Removed some …
- 11:03 AM Ticket #214 (Move TDMS export to this extension) updated by
- (In [1069]) References #214: Move TDMS export to this extension …
- 11:01 AM Changeset [1068] by
- Fixes #214: Move TDMS export to this extension
- 11:01 AM Ticket #214 (Move TDMS export to this extension) closed by
- fixed: (In [1068]) Fixes #214: Move TDMS export to this extension
May 14, 2009:
- 7:05 PM Changeset [1067] by
- Addresses #118. Forcing negative and 0 intensities to be NaNs with 0 …
- 7:05 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1067]) Addresses #118. Forcing negative and 0 intensities to be …
- 5:09 PM Changeset [1066] by
- Preparing for next milestone.
- 1:41 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) updated by
- Replying to martin: > BASE 2.12 is required. > …
- 1:23 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- My best idea so far is to not complicate things too much. I prefer not …
- 1:22 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) reopened by
- BASE 2.12 is required. Build.xml, base-plugins.xml and …
- 12:28 PM Changeset [1065] by
- Reverting changes commit by mistake to README.
- 12:26 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1064]) Addresses #118. Calculate target with median instead of mean.
- 12:26 PM Changeset [1064] by
- Addresses #118. Calculate target with median instead of mean.
- 12:01 PM Changeset [1063] by
- Add qQuantiler to autodetection list.
- 7:39 AM Ticket #207 (Illumina DASL arrays) closed by
- invalid
- 7:26 AM Ticket #210 (net.sf.basedb.normalizers: Add proper 2-channel support to ...) updated by
-
Status, Milestone changed
- 7:26 AM Ticket #183 (Change result storage of qQuantilNormalizer when BASE bioassay set ...) updated by
-
Milestone changed
May 13, 2009:
- 8:09 AM Changeset [1062] by
- Addresses #118. Added support to use either mean or median in target …
- 8:09 AM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1062]) Addresses #118. Added support to use either mean or median …
May 11, 2009:
- 1:23 PM Changeset [1061] by
- References #214: Move TDMS export to this extension The new exporter …
- 1:23 PM Ticket #214 (Move TDMS export to this extension) updated by
- (In [1061]) References #214: Move TDMS export to this extension The …
- 1:06 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) closed by
- fixed: (In [1060]) Fixes #195 Normalizers should ask user for how to …
- 1:06 PM Changeset [1060] by
- Fixes #195 Normalizers should ask user for how to calculate averages
- 12:56 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- Some more questions: 1. Are the columns tab-separated? 2. Can …
- 12:55 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- The text below is from the MeV documentation …
- 12:37 PM Ticket #214 (Move TDMS export to this extension) updated by
-
Status changed
- 12:36 PM Ticket #214 (Move TDMS export to this extension) created by
-
The
BioAssaySetExporteris going through refactoring as described by …
May 8, 2009:
- 3:02 PM Changeset [1059] by
- Use functionality already in yat.
- 12:24 PM Changeset [1058] by
- The normalizer package now depends in PluginUtilites version 0.1
- 12:17 PM Changeset [1057] by
- Tagging version 0.1 of PluginUtilities
- 12:15 PM Changeset [1056] by
- Preparing release 0.1 of PluginUtilities package.
May 7, 2009:
- 2:31 PM Ticket #195 (net.sf.basedb.normalizers: Normalizers should ask user for how to ...) updated by
-
Status changed
- 12:43 AM Changeset [1055] by
- Reverting previuos commit on configure.ac, still requiring 0.5.3
- 12:41 AM Changeset [1054] by
- Cleaned up iterator usage in qQN.cc
- 12:30 AM Changeset [1053] by
- Addresses #208. Fixing typos.
- 12:30 AM Ticket #208 (Revert changeset:1045 when yat bug ...) updated by
- (In [1053]) Addresses #208. Fixing typos.
- 12:28 AM Changeset [1052] by
- 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
- fixed: (In [1052]) Fixes #208. Reverted changeset:1045 and added requirement …
May 6, 2009:
- 5:05 PM Ticket #208 (Revert changeset:1045 when yat bug ...) updated by
-
Status changed
Reverting the change, yat 0.5.3 will be released soon. Now requiring … - 1:15 PM Changeset [1051] by
- Updated documentation on QuantileNormalization.
- 11:11 AM Changeset [1050] by
- Addresses #118. Non-logged input values are expected, geometric mean …
- 11:11 AM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
- (In [1050]) Addresses #118. Non-logged input values are expected, …
- 9:20 AM Changeset [1049] by
- Addresses #206. Last commit destroyed nan fixing in changeset:1045 for …
- 9:20 AM Ticket #206 (net.sf.basedb.normalizers: Make qQuantileNormalization handle missing ...) updated by
- (In [1049]) Addresses #206. Last commit destroyed nan fixing in …
May 5, 2009:
- 2:49 PM Ticket #194 (Default export file names should be more unique) updated by
- Replying to nicklas: > We are already protected against …
May 4, 2009:
- 12:05 PM Ticket #193 (Use one JNLP file for each pre-signed JAR file) updated by
-
Component changed
- 12:00 PM Ticket #212 (Add support for exporting CGH data to MeV) updated by
-
Status changed
- 11:56 AM Ticket #212 (Add support for exporting CGH data to MeV) updated by
- I am thinking that maybe we should also consider moving the MeV TDMS …
- 11:52 AM Ticket #212 (Add support for exporting CGH data to MeV) updated by
-
Milestone changed
- 11:50 AM Ticket #194 (Default export file names should be more unique) updated by
-
Milestone changed
> Of course, the user may change the name manually to something … - 11:46 AM Changeset [1048] by
- Fixes #213: Cannot save MeV options It was caused by #203 and never …
- 11:46 AM Ticket #213 (Cannot save MeV options) closed by
- fixed: (In [1048]) Fixes #213: Cannot save MeV options It was caused by #203 …
- 11:44 AM Ticket #213 (Cannot save MeV options) updated by
-
Milestone changed
- 11:43 AM Ticket #203 (Change source files to UTF-8) updated by
-
Milestone changed
- 11:38 AM Ticket #213 (Cannot save MeV options) updated by
-
Milestone changed
- 11:38 AM Ticket #203 (Change source files to UTF-8) updated by
-
Milestone changed
Apr 30, 2009:
- 11:47 AM Ticket #213 (Cannot save MeV options) created by
- 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
- This is supposed to be straightforward the format is well-defined.
Apr 27, 2009:
- 4:25 PM Ticket #211 (Request: R/G quantile normalization) updated by
-
Type changed
- 4:24 PM Ticket #211 (Request: R/G quantile normalization) created by
- 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 ...) updated by
-
Status changed
- 3:32 PM Ticket #210 (net.sf.basedb.normalizers: Add proper 2-channel support to ...) created by
- That is, keep our old favourite A \propto ln(ch1*ch2) the same value …
- 3:24 PM Changeset [1047] by
- 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
- fixed: (In [1047]) Fixes #206. Missing values in reference now works. Each …
- 1:14 PM Changeset [1046] by
- Debugging should be turned if in repository code.
- 1:08 PM Ticket #180 (Overview plot extensions for Illumina expression) updated by
-
Description changed
- 11:57 AM Ticket #180 (Overview plot extensions for Illumina expression) updated by
-
Description, Summary changed
- 11:31 AM Ticket #209 (Export of data to data repositories such as GEO and ArrayExpress) updated by
-
Description changed
- 11:30 AM Ticket #209 (Export of data to data repositories such as GEO and ArrayExpress) created by
- We should create an export plug-in/extesion for the GEO repository, …
Note:
See TracTimeline
for information about the timeline view.
