Specified element is out of bounds error of MDS Plugin within Tassel GUI

Denis

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Feb 17, 2022, 2:00:49 PM2/17/22

to TASSEL - Trait Analysis by Association, Evolution and Linkage

Hello,

I got the error:

"[Thread-15] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.18 Date: December 10, 2015

[Thread-15] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 5412 MB
[Thread-15] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_40
[Thread-15] INFO net.maizegenetics.tassel.TasselLogging - OS: Windows 8.1
[Thread-15] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8
[Thread-15] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.tassel.TasselLogging: time: �� 17, 2022 21:52:15
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.dna.snp.CoreGenotypeTable
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: node type: class net.maizegenetics.analysis.distance.IBSDistanceMatrix
[AWT-EventQueue-0] INFO net.maizegenetics.tassel.DataTreePanel - initSelectionListener: Table Report Size: 5700
[Thread-16] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin: time: �� 17, 2022 21:53:52
[Thread-16] INFO net.maizegenetics.plugindef.AbstractPlugin -
MultiDimensionalScalingPlugin Parameters
axes: 5

[Thread-16] DEBUG net.maizegenetics.plugindef.AbstractPlugin - Specified element is out of bounds: 0 280
java.lang.IllegalArgumentException: Specified element is out of bounds: 0 280
at org.ejml.data.DenseMatrix64F.get(Unknown Source)
at org.ejml.ops.SpecializedOps.subvector(Unknown Source)
at net.maizegenetics.matrixalgebra.Matrix.EJMLDoubleMatrix.column(EJMLDoubleMatrix.java:67)
at net.maizegenetics.stats.PCA.ClassicMds.calculatePCs(ClassicMds.java:85)
at net.maizegenetics.stats.PCA.ClassicMds.<init>(ClassicMds.java:25)
at net.maizegenetics.analysis.distance.MultiDimensionalScalingPlugin.processData(MultiDimensionalScalingPlugin.java:52)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)"

Could you advise me please how can i fix it?

Regards,

Denis

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Feb 17, 2022, 3:18:06 PM2/17/22

to TASSEL - Trait Analysis by Association, Evolution and Linkage

I've imported the distance matrix i got in Tassel GUI to R environment. The cmdscale() R function works fine on the matrix. So i still can't figure out what is wrong.

Regards,

Denis

четверг, 17 февраля 2022 г. в 22:00:49 UTC+3, Denis:

Terry Casstevens

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Feb 17, 2022, 3:42:48 PM2/17/22

to Tassel User Group

I recommend updating your version of TASSEL. Your version came out
over 6 years ago.

Do you have a screen shot?

If you want to send me your file private, I will try it.

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Denis

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Feb 18, 2022, 1:50:57 PM2/18/22

to TASSEL - Trait Analysis by Association, Evolution and Linkage

Hi Terry,

Thank you very much for your quick reply. I've solved it by updating Tassel to the latest version.

Regards,

Denis

четверг, 17 февраля 2022 г. в 23:42:48 UTC+3, Terry:

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