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
>>>
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>>
>> ===============================================
>> 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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===============================================
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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