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Ticket Summary Owner Type Priority Milestone Component
#1 Reformat plug-ins archive/download page to look like the rest of the trac environment. Jari Häkkinen task minor tracpages
#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
#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
#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
#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
#45 PLIER - Probe Logaritmic Intensity ERror Peter Johansson task major se.lu.thep.affymetrix
#46 RMAExpress wiki page Peter Johansson task minor tracpages
#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
#51 add configure options to WeNNI Peter Johansson task major se.lu.thep.wenni
#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
#57 --with-base configure option [default /usr/local/base] Peter Johansson task major se.lu.thep.wenni
#58 --base-plugindir configure option Peter Johansson task major se.lu.thep.wenni
#59 --with-gsl configure option Peter Johansson task minor se.lu.thep.wenni
#60 explain how to run wenni (base1 version) against a base_devkit Peter Johansson task major se.lu.thep.wenni 0.7 se.lu.thep.wenni
#61 change structure of tags Jari Häkkinen task blocker tracpages
#62 make check does not work Peter Johansson defect major se.lu.thep.wenni
#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
#65 version number in BASE1 plugin is not updated automatically Peter Johansson enhancement minor 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
#72 NNIFileConverter should not be installed in base2 mode Peter Johansson task minor se.lu.thep.wenni
#77 Update information about webservice defect major ZZ Other tickets tracpages
#79 Center on assay (se.lu.onk.Center) olle task major ZZ Other tickets se.lu.onk series plug-ins
#83 ReplicateError: Error in ReplicateError Jari Häkkinen defect major se.lu.onk series plug-ins
#84 Change parameter in ReplicateError (se.lu.onk.ReplicateError) olle enhancement major ZZ Other tickets se.lu.onk series plug-ins
#89 Installation program and documentation Johan Enell task critical Illumina package v1.0 net.sf.basedb.illumina
#90 Create array design from a bgx-file Martin Svensson task critical Illumina package v1.0 net.sf.basedb.illumina
#91 Import Illumina Bead Summary(IBS) files as raw data Nicklas Nordborg task major 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
#94 Import reporter annotations from bgx files Nicklas Nordborg task major Illumina package v1.0 net.sf.basedb.illumina
#95 Intensity calculator for Illumina expression data Jari Häkkinen task major Illumina package v1.1 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
#99 The tagging system of the repository should be changed Jari Häkkinen enhancement major tracpages
#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
#102 Intensity calculator for Illumina SNP data Nicklas Nordborg task major Illumina package v1.0 net.sf.basedb.illumina
#103 Create example extensions Nicklas Nordborg task blocker Extension examples v1.0 net.sf.basedb.examples.extensions
#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
#105 Complete the move of the example code from BASE. Nicklas Nordborg task blocker Plugin examples v2.6 net.sf.basedb.examples.plugins
#106 Move the example web services code from the BASE server Nicklas Nordborg task major Web services examples v2.6 net.sf.basedb.examples.webservices
#107 Move the MEV specific code from BASE Nicklas Nordborg task blocker MEV Launcher v1.0 net.sf.basedb.mev
#108 Update information about MEV on the BASE-hacks site Nicklas Nordborg task major MEV Launcher v1.0 net.sf.basedb.mev
#109 Add information to the wiki page on how to give feedback on the Illumina package Nicklas Nordborg task 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
#112 Illumina plug-in installer script fails (in some cases) Martin Svensson defect major Illumina package v1.2 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
#114 Implement FTP Server Nicklas Nordborg task blocker net.sf.basedb.ftp
#116 Make the MEV launcher extension aware of bioassaysets that store data in file Nicklas Nordborg enhancement major MEV Launcher v1.1 net.sf.basedb.mev
#117 Create average nomralization plug-in Martin Svensson task major Normalization package v1.0 net.sf.basedb.normalizers
#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
#121 BGX-importer should 0-pad Array_Address_ID if the BGX-file doesn't have done that already Martin Svensson enhancement major Illumina package v1.2 net.sf.basedb.illumina
#122 Add wiki-page for Normalization-package Martin Svensson task major Normalization package v1.0 net.sf.basedb.normalizers
#123 Update BasePlug-ins' firstpage Martin Svensson defect major tracpages
#124 files in Normalization package state they're are part of Illumina package Martin Svensson defect trivial Normalization package v1.0 net.sf.basedb.normalizers
#127 Update to final release of Apache Mina FTP server Nicklas Nordborg task critical FTP Server v1.0 net.sf.basedb.ftp
#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
#138 Importing data for multiple raw bioassays in one step Nicklas Nordborg enhancement critical Illumina package v1.2 net.sf.basedb.illumina
#140 Add support in build.xml for automatic download of BASE jar files Nicklas Nordborg enhancement minor Illumina package v1.2 net.sf.basedb.illumina
#141 Rank invariant should not support configurations Martin Svensson defect critical Normalization package v1.0 net.sf.basedb.normalizers
#142 Illumina installer plugin cannot be installed in some cases Martin Svensson defect major Illumina package v1.2 net.sf.basedb.illumina
#143 Illumina plug-in package installer requests wrong permissions Martin Svensson defect major Illumina package v1.2 net.sf.basedb.illumina
#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
#150 Fix layout of DetectionPValue.java Nicklas Nordborg task minor Illumina package v1.2 net.sf.basedb.illumina
#151 Use two queries instead of one in DetectionPValue.run() method Nicklas Nordborg enhancement critical Illumina package v1.2 net.sf.basedb.illumina
#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
#156 Compilation fails in base2 test phase of 'make maintainer-check' Peter Johansson defect 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
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