Hi Bob, Just wanted to tell you that I've successfully executed the clustering from Base1. As you mentioned the export wrote the external id wrong. It should be reporterId. It has been fixed in the Base2.4 branch.
/Johan 12 sep 2007 kl. 13.36 skrev Bob MacCallum: > > [note: minor bug report buried deep in this email] > >> Now I'm just having some problems with the BASE1/BASE2 column names. >> >> At last google and the mailing list help me out: >> http://www.mail-archive.com/basedb-users@lists.sourceforge.net/ >> msg00725.html >> >> It looks like I just have to create an extra value column called >> ratio1_2 > > actually I need a "formula" exactly as the mail suggests. > > > But I'm still getting a problem: > > > Status Error: /usr/local/base_dir/base2dev_plugins/base1plugins/ > basehclust: Missing reporterId/assayData columns or ratio field > > Job parameters > Assay distance metric Pearson > New cluster point center of mass > Gene distance metric Pearson > Plugin directory /home/maccallr/Analysis Hierarchical clustering > ratioColumn ratio1_2 > section clustering settings > Bioassay set background subtracted medians > Plugin configuration parameters > Parameter version 7 (7) > execName clusteringscript > Plugin executables path /usr/local/base_dir/base2dev_plugins/ > base1plugins > geneAverages true > jobParameters [snip: imported from working base1 instance - no > changes made] > leaveStdin true > leaveStdout false > maxChannels 2 > minChannels 2 > serialFormat false > usedColumns reporterId > usedFields ratio1_2 > versionNumber 1.1 > > > Since Base1PluginExecuter uses > BioAssaySetExporter.exportBaseFileMatrix to > create a BASEfile, I tried to do this manually and get > "columns externalId assayData" > rather than > "columns reporterId assayData" > which I guess the basehclust binary is expecting? > > Here's a snippet of the BASEfile I manually exported. See how the > ratio1_2 > column is all present and correct (thanks to the formula). > > > BASEfile > section assays > count 12 > columns id name Generation OrganismPart > annotationColumns Generation OrganismPart > % > 263 carcass_g1-cy3_SR-cy5 1 carcass > 264 carcass_g1-cy5_SR-cy3 1 carcass > 265 carcass_g3-cy5_SR-cy3 3 carcass > 266 head_g1-cy3_SR-cy5 1 head > 267 head_g1-cy5_SR-cy3 1 head > 268 head_g3-cy5_SR-cy3 3 head > 269 midgut_g1-cy3_SR-cy5 1 midgut > 270 midgut_g1-cy5_SR-cy3 1 midgut > 271 midgut_g3-cy5_SR-cy3 3 midgut > 272 ovaries_g1-cy3_SR-cy5 1 ovaries > 273 ovaries_g1-cy5_SR-cy3 1 ovaries > 274 ovaries_g3-cy5_SR-cy3 3 ovaries > > section spots > channels 2 > assayFields ratio1_2 > columns externalId assayData > assays 263 264 265 266 267 268 269 270 > 271 272 273 274 > count 21100 > % > 4A3B-AAB-A-06 5.7225670458895 3.1218635882757 3.0588992108785 > 0.2639156720298 4.0223276353137 6.675902576748 3.4137582490339 > 2.3933277183965 2.7949516801256 2.7989004774074 2.481474953736 > 2.9725981696501 > 4A3B-AAB-A-12 2.6034823374857 1.8699111228203 2.1851485479522 > 0.46444012021543 1.5953635012332 2.6418038900175 1.1084148689112 > 0.81114689236237 1.2586586018848 1.3185744749523 1.3753473626496 > 1.0045607051797 > 4A3B-AAB-C-06 2.1968544953519 1.9939638540184 ... > > > > I then tried to create a "reporterId" formula in the same way, but > this caused > an uncaught exception (in the tomcat logs) when I try to view the > column in > experiment explorer: > > > 12:05:43,237 ERROR [jsp]:253 - Servlet.service() for servlet jsp > threw exception > java.lang.ClassCastException: java.lang.String cannot be cast to > java.lang.Number > at net.sf.basedb.util.formatter.NumberFormatter.format > (NumberFormatter.java:35) > at net.sf.basedb.clients.web.taglib.table.Cell.doEndTag > (Cell.java:231) > at > org.apache.jsp.views.experiments.explorer.view.view_jsp._jspService > (view_jsp.java:1450) > > > Not surprisingly a text column doesn't work too well in a formula. > > > It looks like I should recompile basehclust to look for externalId > instead of > reporterId. This seems trivial having grepped the source code. > Any thoughts? > > cheers, > Bob. > > > > >> >> cheers, >> Bob. >> >> Johan Enell writes: >>> Hj Bob, >>> >>> The clustering from Base1 will not work in Base2. Or more precisely, >>> you will be able to run the plugin but you wont be able to se the >>> result. The visualization page in Base1 was a specific php page for >>> that plugin and we didn't want a solution like that in Base2. >>> >>> >>> When you configure Base1 plugins you should always start of from a >>> base1 plugin configuration file. From the plugin page in Base1 you >>> will find an export link with each plugin. Use that file to >>> configure >>> the Base1PluginExecuter. >>> >>> /Johan >>> >>> >>> 11 sep 2007 kl. 16.58 skrev Bob MacCallum: >>> >>>> >>>> Hi, >>>> >>>> I was trying to find out if base1's hierarchical clustering would >>>> run under >>>> base2 - and got to the point where I need to provide parameter >>>> settings as >>>> XML. I could spend an hour figuring this out by hand (e.g. from >>>> the examples >>>> on the BASE2 demo server) but I'm convinced there's an easier way. >>>> I've >>>> searched the plugin site for documentation. Could someone help >>>> please? >>>> >>>> Since the hierarchical clustering isn't on the BASE2 demo server, >>>> does that >>>> mean it doesn't work? >>>> >>>> We know that there won't be any display tools available in BASE2 >>>> for this, but >>>> we can work with the PNGs and assorted text files. >>>> >>>> many thanks, >>>> Bob. >>>> >>>> >>>> >>>> -- >>>> Bob MacCallum | VectorBase Developer | Kafatos/Christophides >>>> Groups | >>>> Division of Cell and Molecular Biology | Imperial College London | >>>> Phone +442075941945 | Email [EMAIL PROTECTED] >>>> >>>> ------------------------------------------------------------------- >>>> --- >>>> --- >>>> This SF.net email is sponsored by: Microsoft >>>> Defy all challenges. Microsoft(R) Visual Studio 2005. >>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>> _______________________________________________ >>>> The BASE general discussion mailing list >>>> basedb-users@lists.sourceforge.net >>>> unsubscribe: send a mail with subject "unsubscribe" to >>>> [EMAIL PROTECTED] >>> >>> >>> -------------------------------------------------------------------- >>> ----- >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2005. >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> _______________________________________________ >>> The BASE general discussion mailing list >>> basedb-users@lists.sourceforge.net >>> unsubscribe: send a mail with subject "unsubscribe" to >>> [EMAIL PROTECTED] >> >> -- >> Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | >> Division of Cell and Molecular Biology | Imperial College London | >> Phone +442075941945 | Email [EMAIL PROTECTED] >> >> --------------------------------------------------------------------- >> ---- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2005. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> The BASE general discussion mailing list >> basedb-users@lists.sourceforge.net >> unsubscribe: send a mail with subject "unsubscribe" to >> [EMAIL PROTECTED] > > -- > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | > Division of Cell and Molecular Biology | Imperial College London | > Phone +442075941945 | Email [EMAIL PROTECTED] > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
