Hi, I have created a combo box for the reference group. Before you run the heat map module in MZmine you should install the package "gplots" in R.
Cheers, Sandra On 08/17/2011 11:34 AM, Tomas Pluskal wrote: Hi Sandra, When I did not set the reference group correctly, I got this exception: java.lang.ArrayIndexOutOfBoundsException: 2 at net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapTask.groupingDataset(HeatMapTask.java:550) at net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapTask.run(HeatMapTask.java:102) at net.sf.mzmine.taskcontrol.impl.WorkerThread.run(WorkerThread.java:60) When I set the reference group correctly, I got this one: java.lang.IllegalStateException: The "gplots" R package couldn't be loaded - is it installed in R? at net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapTask.run(HeatMapTask.java:137) at net.sf.mzmine.taskcontrol.impl.WorkerThread.run(WorkerThread.java:60) By the way, setting of the reference parameter would be better using a combo box, what do you think? By the way #2, on any error your module just says "R error during the heat map creation". More detailed error message would be useful. Cheers, Tomas On Aug 11, 2011, at 4:04 PM, Castillo Sandra wrote: Hi Tomas, I will solve this exception. To run the heat map plot module first you have to define the sample groups in the sample parameter option (project->set sample parameters) (at least two groups) and define one of these groups as the reference group. If the option "P-value legend" is selected, only the groups will be plot. If it is not selected, the samples will be plotted individually. Sandra On 08/11/2011 04:51 AM, Tomas Pluskal wrote: Hi Sandra, I tried to run it, but I got this exception: [10:49:42|FINEST|MainMenu]: Starting module Heat map plot with parameters Output name: /tmp/aa.png, Output file type: png, Sample parameter: No parameters defined, Group of reference: asdas, Only identified rows: false, Use peak area: true, Scaling: true, Log: true, Show control samples: true, P-value legend: true, Size p-value legend: 5, Height: 10, Width: 10, Column margin: 10, Row margin: 10 Exception in thread "AWT-EventQueue-0" java.lang.NegativeArraySizeException at net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapTask.groupingDataset(HeatMapTask.java:463) at net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapTask.<init>(HeatMapTask.java:74) at net.sf.mzmine.modules.peaklistmethods.dataanalysis.heatmaps.HeatMapModule.runModule(HeatMapModule.java:50) at net.sf.mzmine.desktop.impl.MainMenu.actionPerformed(MainMenu.java:338) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.AbstractButton.doClick(AbstractButton.java:389) at com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95) at java.awt.MenuItem.processActionEvent(MenuItem.java:627) at java.awt.MenuItem.processEvent(MenuItem.java:586) at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:337) at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:325) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:638) at java.awt.EventQueue$1.run(EventQueue.java:636) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$2.run(EventQueue.java:652) at java.awt.EventQueue$2.run(EventQueue.java:650) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:649) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) Tomas On Aug 10, 2011, at 11:02 PM, Castillo Sandra wrote: Hi, I just committed a new module to plot heat maps using R. Any comment? Sandra ------------------------------------------------------------------------------ uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net<mailto:Mzmine-devel@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/mzmine-devel =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan TEL: +81-98-966-8684 ------------------------------------------------------------------------------ Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-dev2dev_______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net<mailto:Mzmine-devel@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/mzmine-devel =============================================== Tomas Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan TEL: +81-98-966-8684
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