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Ticket Summary Owner Type Priority Milestone Component
#2 enhance group/sort command in ReplicateErrorWA Johan Enell enhancement major onk.lu.se
#3 Create replicates with more then 2 spots Johan Enell enhancement major onk.lu.se
#26 Print result table as Output txt Johan Enell enhancement trivial se.lu.onk.ztest
#27 No limit on result list Johan Enell defect trivial se.lu.onk.ztest
#28 Create plot observed/expected Johan Enell enhancement minor se.lu.onk.ztest
#29 Create plot FDR vs rank Johan Enell enhancement minor se.lu.onk.ztest
#30 Create combination plot Johan Enell enhancement minor se.lu.onk.ztest
#31 More reporter info Johan Enell enhancement trivial se.lu.onk.ztest
#32 Create histogram plot Johan Enell enhancement minor se.lu.onk.ztest
#33 Change normsdist calculations Johan Enell enhancement major se.lu.onk.ztest
#37 Add box-plot output Johan Enell enhancement major se.lu.onk.smooth
#38 Parameterparser splits the annotations values parameter incorrect Johan Enell defect major onk.lu.se
#40 Create virtual bioassay containing analysis results Johan Enell enhancement major se.lu.onk.ztest
#89 Installation program and documentation Johan Enell task critical Illumina package v1.0 net.sf.basedb.illumina
#1 Reformat plug-ins archive/download page to look like the rest of the trac environment. Jari Häkkinen task minor tracpages
#12 RMAExpress plug-n on mac does not free temporary files when throwing an IOException Jari Häkkinen defect major se.lu.thep.affymetrix
#13 RMAExpress does not exit gracefully if no configuration was available Jari Häkkinen defect major se.lu.thep.affymetrix
#14 RMAExpress: make 'make dist' to set the proper VERSION Jari Häkkinen defect major se.lu.thep.affymetrix
#15 RMAExpress: Instructions on how to update Jari Häkkinen defect major se.lu.thep.affymetrix
#17 Export RMA bioassayset as a tab delimited file Jari Häkkinen enhancement minor se.lu.thep.affymetrix
#21 Make installation from the packaged source distribution work Jari Häkkinen defect major se.lu.thep.affymetrix
#42 Add sample extended-properties.xml and configuration files needed for BASE plug-ins. Jari Häkkinen enhancement minor se.lu.thep.affymetrix
#44 Add information on how to compile RMAExpressConsole to the RMAExpress plug-in page Jari Häkkinen enhancement major se.lu.thep.affymetrix
#47 A new release of RMAExpress was released 25 March 2007. Jari Häkkinen defect major se.lu.thep.affymetrix
#49 Rename wiki:onk.lu.se.ZTest to wiki:se.lu.onk.ZTest Jari Häkkinen task major tracpages
#53 update INSTALL Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#54 update README Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#55 update ChangeLog Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#61 change structure of tags Jari Häkkinen task blocker tracpages
#63 make distcheck should work Jari Häkkinen enhancement major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#64 configure does not find basefile.h Jari Häkkinen defect minor se.lu.thep.wenni 0.7 se.lu.thep.wenni
#67 The plier and rmaexpress plug-ins does not work in a Microsoft enviornment Jari Häkkinen defect major se.lu.thep.affymetrix
#68 Update the documentation to explain what should be done to get the plug-in to work in Microsoft windows Jari Häkkinen task major se.lu.thep.affymetrix
#69 DBControl bad code style, beware and fix it! Jari Häkkinen defect critical se.lu.thep.affymetrix
#83 ReplicateError: Error in ReplicateError Jari Häkkinen defect major se.lu.onk series plug-ins
#95 Intensity calculator for Illumina expression data Jari Häkkinen task major Illumina package v1.1 net.sf.basedb.illumina
#99 The tagging system of the repository should be changed Jari Häkkinen enhancement major tracpages
#104 Add information that BASE2WSClient.jar is needed to compile the plug-ins Jari Häkkinen defect major Illumina package v1.1 net.sf.basedb.illumina
#110 Illumina detection P-value plug-in Jari Häkkinen enhancement major Illumina package v1.1 net.sf.basedb.illumina
#111 Update Illumina wiki pages and related documentation before release Jari Häkkinen task major Illumina package v1.1 net.sf.basedb.illumina
#113 Add support for more variations of Illumina detection P-value calculations Jari Häkkinen enhancement major Illumina package v1.4 net.sf.basedb.illumina
#118 Create qQuantile normalizer (aka cubic-spline normalizer) Jari Häkkinen task major Normalization package v1.1 net.sf.basedb.normalizers
#120 Create a normalization plug-in package. Jari Häkkinen task major Normalization package v1.1 net.sf.basedb.normalizers
#129 ReplicateError: Create a se.lu.onk.ReplicateError module Jari Häkkinen task major se.lu.onk series plug-ins
#131 se.lu.onk.BaseFile should be its own package Jari Häkkinen task major se.lu.onk series plug-ins
#132 ReplicateError: In witihn assays only one position of accepted replicate pairs are kept Jari Häkkinen defect critical se.lu.onk series plug-ins
#133 ReplicateError: The plug-in adds new entries to the stdout.txt for reporters that had null values in stdin.txt Jari Häkkinen enhancement major onk.lu.se
#134 BaseFile: public void resetDataPosition(BASEFileSection section) positions the file pointer one line too far Jari Häkkinen defect major onk.lu.se
#136 ReplicateError: Make version info to propagate automatically during ant package Jari Häkkinen defect major se.lu.onk series plug-ins
#137 Create a se.lu.onk.MergeBioAssay module Jari Häkkinen defect major se.lu.onk series plug-ins
#145 GPL3 for WeNNI Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#146 Change references to lev.thep.lu.se to something more appropriate Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#148 BASE1 configuration: execname should be set automatically during build Jari Häkkinen enhancement major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#152 Setting bindir in configure.ac destroys make distcheck Jari Häkkinen defect major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#154 wenni compiling WeNNI.java requires -encoding option to the compiler Jari Häkkinen task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#157 Create a se.lu.onk.Center module Jari Häkkinen defect major se.lu.onk series plug-ins
#159 Create a se.lu.onk.VirtualArray module Jari Häkkinen task major ZZ Other tickets se.lu.onk series plug-ins
#165 Create quantile normalizer Jari Häkkinen task major Normalization package v1.0 net.sf.basedb.normalizers
#167 (net.sf.basedb.normalizers) Average normalizer should use geometric mean Jari Häkkinen enhancement major Normalization package v1.0 net.sf.basedb.normalizers
#184 qQuantileNormalizer should update progress bar Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#186 qQuantileNormalizer method storeResult must be reimplemented Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#187 qQuantileNormalizer should allow user to select the normaliztion reference assay set Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#190 net.sf.basedb.normalizers: Add target that tries to build qQN if requested Jari Häkkinen task major Normalization package v1.1 net.sf.basedb.normalizers
#191 net.sf.basedb.normalizers: qQN should support standard options ... Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#197 net.sf.basedb.normalizers: Add abort functionaly to qQuantileNormalizers Jari Häkkinen task major Normalization package v1.1 net.sf.basedb.normalizers
#204 Add option to include all available negative controls in detection P-value calculation Jari Häkkinen enhancement major Illumina package v1.4 net.sf.basedb.illumina
#205 Change link README_PluginDetails to point to tags at next release Jari Häkkinen defect major Illumina package v1.4 net.sf.basedb.illumina
#206 net.sf.basedb.normalizers: Make qQuantileNormalization handle missing values Jari Häkkinen enhancement major Normalization package v1.1 net.sf.basedb.normalizers
#208 Revert changeset:1045 when yat bug http://dev.thep.lu.se/yat/ticket/535 is fixed Jari Häkkinen task major Normalization package v1.1 net.sf.basedb.normalizers
#227 Illumina detection P-value plug-in description must be improved Jari Häkkinen Request major Illumina package v1.4 net.sf.basedb.illumina
#230 Illumina detection P-value Control outlier cut-off parameter cannot be zero Jari Häkkinen Request major Illumina package v1.4 net.sf.basedb.illumina
#231 Illumina detection P-value fails if no negative controls are available in the bio assayset Jari Häkkinen Request major Illumina package v1.4 net.sf.basedb.illumina
#235 Illumina package: Add instructions on how to remove 'Illumina' raw data type from the server Jari Häkkinen enhancement major Illumina package v1.4 net.sf.basedb.illumina
#247 net.sf.basedb.normalizers: qQuantileNormalization crashes when normalizing filtered bioassay sets Jari Häkkinen defect major Normalization package v1.1 net.sf.basedb.examples.extensions
#248 net.sf.basedb.illumina: The background correction plug-in should store the background intensity Jari Häkkinen enhancement major Illumina package v1.5 net.sf.basedb.illumina
#251 net.sf.basedb.illumina: Describe the overview plots in README_PluginDetails Jari Häkkinen task major Illumina package v1.5 net.sf.basedb.illumina
#252 net.sf.basedb.illumina: The background correction plug-in should store the reporters used for background calculations Jari Häkkinen Request major Illumina package v1.5 net.sf.basedb.illumina
#255 link to APT plug-in times out Jari Häkkinen defect trivial ZZ Other tickets tracpages
#259 Apply patch provided in the BASE dev list to Tab2MageExporter Jari Häkkinen Request major ZZ Other tickets not classified
#263 Release version 1.0 of the Agilent plug-in package Jari Häkkinen task critical Agilent package 1.0 net.sf.basedb.agilent
#270 lev.thep.lu.se website down? Jari Häkkinen defect major not classified
#273 Bug in detection p-value Jari Häkkinen defect major Illumina package v1.5.1 net.sf.basedb.illumina
#295 Configuration file for VirtualArray is missing a tab in 'desc' field Jari Häkkinen defect major VirtualArray 1.2 se.lu.onk series plug-ins
#297 VirtualArray should activate "average on reporter" setting Jari Häkkinen defect minor VirtualArray 1.2 se.lu.onk series plug-ins
#298 VirtualArray can work with 1-channel data Jari Häkkinen enhancement minor VirtualArray 1.2 se.lu.onk series plug-ins
#301 Make sure installation instructions for VirtualArray are correct Jari Häkkinen defect minor VirtualArray 1.2 se.lu.onk series plug-ins
#321 reggie 1.4: Consentform cannot be registered if date is missing Jari Häkkinen defect major Reggie v1.5 net.sf.basedb.reggie
#340 Set subtype for all biomaterial items Jari Häkkinen task blocker Reggie v2.1 net.sf.basedb.reggie
#394 Change weight table order in Partition wizard Jari Häkkinen Request major Reggie v2.7 not classified
#400 Update NoSpecimen items with values for laterality Jari Häkkinen task major Reggie v2.7 net.sf.basedb.reggie
#652 New location of BASE JAR files Jari Häkkinen task critical not classified
#799 TypeError: bestStain is null in case summary Jari Häkkinen defect minor Reggie v3.5 net.sf.basedb.reggie
#1152 Switch to Java 11 and BASE 3.15 Jari Häkkinen task major Open Grid Scheduler service v1.3 net.sf.basedb.opengrid
#90 Create array design from a bgx-file Martin Svensson task critical Illumina package v1.0 net.sf.basedb.illumina
#93 Illumina SNP validator and meta-data extractor Martin Svensson task critical Illumina package v1.0 net.sf.basedb.illumina
#98 Implement validator and metadata extractor plug-in for BGX files Martin Svensson task major Illumina package v1.0 net.sf.basedb.illumina
#100 Add Illumina SNP platform to the installation program Martin Svensson enhancement critical Illumina package v1.0 net.sf.basedb.illumina
#101 Import plug-in for SNP raw data Martin Svensson task critical Illumina package v1.0 net.sf.basedb.illumina
#112 Illumina plug-in installer script fails (in some cases) Martin Svensson defect major Illumina package v1.2 net.sf.basedb.illumina
#117 Create average nomralization plug-in Martin Svensson task major Normalization package v1.0 net.sf.basedb.normalizers
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