Hi,
I am tring to perform hierarchical clustering on a very high number of features. I am not doing gene expression analysis but I am performing analysis on scaffold coverage. Since the number of features we are considering is very high (more than 40000) the software is not able to complete clustering.
I tried different versions of the software both on linux (24 Gbite RAM) and windows (8 Gbite RAM) platforms. I set the -Xmx parameter in the ".sh" executable (linux version) to 8Gb to allow analysis of large number of features but the software stops without producing the final tree and gave an error.
Is there a maximum number of features that can be clusterized using TMEV?
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May be more information about your setup will help. Java 32bits or 64bits? Oracle Java? Once you modified options of the .sh/.bat file, have you checked that the options have been taken into account in the "system information" of the "MultiExperiment Viewer" window?
HTH
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I have been experiencing similar problem - I have a 16Gb RAM in my desktop
but I was unable to utilize it
although I have changes the bat file setting. MeV was not able to process
more than 17K genes (Affy microarray data)
May be more information about your setup will help. Java 32bits or 64bits?
Oracle Java? Once you modified options of the .sh/.bat file, have you
checked that the options have been taken into account in the "system
information" of the "MultiExperiment Viewer" window?
HTH
--
Yuriy Gusev, Ph.D.
Senior Bioinformatics Scientist
Innovation Center for Biomedical Informatics (ICBI)
Georgetown University Medical Center
2115 Wisconsin Ave NW,
Suite 110
Washington DC 20007
Tel. (202) 687-5094
Fax (202) 687-5011
Email: yg63@georgetown.edu
Website:icbi.georgetown.edu/
Hi,
I am tring to perform hierarchical clustering on a very high number of features. I am not doing gene expression analysis but I am performing analysis on scaffold coverage. Since the number of features we are considering is very high (more than 40000) the software is not able to complete clustering.
I tried different versions of the software both on linux (24 Gbite RAM) and windows (8 Gbite RAM) platforms. I set the -Xmx parameter in the ".sh" executable (linux version) to 8Gb to allow analysis of large number of features but the software stops without producing the final tree and gave an error.
Is there a maximum number of features that can be clusterized using TMEV?
Hi,
I am having this issue as well and I have seen quite a few other people having this problem. Can we get some feedback from a developer?
May be more information about your setup will help. Java 32bits or 64bits? Oracle Java? Once you modified options of the .sh/.bat file, have you checked that the options have been taken into account in the "system information" of the "MultiExperiment Viewer" window?
HTH
I have been experiencing similar problem - I have a 16Gb RAM in my desktop
but I was unable to utilize it
although I have changes the bat file setting. MeV was not able to process
more than 17K genes (Affy microarray data)
On Wed, Dec 10, 2014 at 12:40 PM, S Granjeaud sgranjeaud@users.sf.net
wrote:
--
Yuriy Gusev, Ph.D.
Senior Bioinformatics Scientist
Innovation Center for Biomedical Informatics (ICBI)
Georgetown University Medical Center
2115 Wisconsin Ave NW,
Suite 110
Washington DC 20007
Tel. (202) 687-5094
Fax (202) 687-5011
Email: yg63@georgetown.edu
Website:icbi.georgetown.edu/