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Changwon Yoo, S.M., Ph.D., PI

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Datasets

Postby meninonas » Fri Jan 23, 2015 9:55 pm

Dr. Yoo,

Please find attached the CSV file for the Cell Cycle. I tried running the code by removing the commented line; nevertheless, it still gave the following error:

Code: Select all
-----------------------------------------------------------------------------
                                 ERROR DETAILS
-----------------------------------------------------------------------------
- Banjo                        Bayesian Network Inference with Java Objects -
- Release 2.2.0                                                 15 Apr 2008 -
- Licensed from Duke University                                             -
- Copyright (c) 2005-08 by Alexander J. Hartemink                           -
- All rights reserved                                                       -
-----------------------------------------------------------------------------
- Project:                                               banjo static example
- User:                                                                  demo
- Dataset:                                           33-vars-320-observations
- Notes:                                    static bayesian network inference
-----------------------------------------------------------------------------

[ERROR: Banjo 2.2.0, 2/5/15 10:52:51 PM]
The following info is provided to assist in trouble-shooting:
The text line ' 0' in 'static.mandatory.str' does not contain enough information to specify a variable and its parent info.

(Warning (dev)) The number of supplied variable names (132) needs to match the number of variables (123); Banjo defaults to the variable index numbers instead.

Stack trace info:

edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.loadStructureFile(EdgesAsArrayWithCachedStatistics.java:2862)
edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.<init>(EdgesAsArrayWithCachedStatistics.java:633)
edu.duke.cs.banjo.bayesnet.BayesNetManager.<init>(BayesNetManager.java:273)
edu.duke.cs.banjo.learner.SearcherSimAnneal.setupSearch(SearcherSimAnneal.java:1092)
edu.duke.cs.banjo.learner.SearcherSimAnneal.<init>(SearcherSimAnneal.java:723)
edu.duke.cs.banjo.application.BanjoThreadHandler.<init>(BanjoThreadHandler.java:115)
edu.duke.cs.banjo.application.Banjo.runMultipleInstances(Banjo.java:200)
edu.duke.cs.banjo.application.Banjo.execute(Banjo.java:150)
edu.duke.cs.banjo.application.Banjo.main(Banjo.java:447)

-----------------------------------------------------------------------------
                           End of error notification
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
(Final Checkpoint, after post-processing) A final check revealed the following issues that were encountered during Banjo's execution:
-----------------------------------------------------------------------------
(Post-processing) Postprocessing cannot proceed because we can't process the high score network(s).


I'll go over the settings with you tomorrow.
Attachments
Cell Cycle.csv
(231.36 KiB) Downloaded 134 times
Last edited by meninonas on Thu Feb 05, 2015 11:56 pm, edited 7 times in total.
meninonas
 
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Re: Datasets

Postby meninonas » Mon Jan 26, 2015 7:30 pm

Dr. Yoo,

I installed Banjo on the Virtual Machine and on the computer and the following error was given to me:

Code: Select all
(Post-processing) Postprocessing cannot proceed because we can't process the high score network(s).
meninonas
 
Posts: 137
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Re: Datasets

Postby cwyoo » Tue Jan 27, 2015 11:45 am

meninonas wrote:Dr. Yoo,

I installed Banjo on the Virtual Machine and on the computer and the following error was given to me:

Code: Select all
(Post-processing) Postprocessing cannot proceed because we can't process the high score network(s).


Please install banjo in path4 machine.
cwyoo
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Re: Datasets

Postby meninonas » Tue Jan 27, 2015 12:35 pm

Dr. Yoo,

I installed Banjo on the Virtual Machine and on the computer and the following error was given to me:

Code: Select all
-----------------------------------------------------------------------------
(Final Checkpoint, after post-processing) A final check revealed the following issues that were encountered during Banjo's execution:
-----------------------------------------------------------------------------
(Post-processing) Postprocessing cannot proceed because we can't process the high score network(s).
meninonas
 
Posts: 137
Joined: Tue Jun 24, 2014 3:25 pm
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Re: Datasets

Postby meninonas » Tue Jan 27, 2015 1:58 pm

Dr. Yoo,

I just wanted to reiterate. I am going to create another dataset where there are going to be three columns per gene with the following names:

    GENENAME_EXP with three states (UP, DOWN, and everything else)

    GENENAME_AMP with two states (AMP;UP/DOWN; and everything else)

    GENENAME_MUT with two states (MUT/HOMDEL;UP/DOWN; and everything else)

If so, when I come back tomorrow, I'll set it up as such and run it.
meninonas
 
Posts: 137
Joined: Tue Jun 24, 2014 3:25 pm
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Re: Datasets

Postby cwyoo » Tue Jan 27, 2015 5:36 pm

meninonas wrote:Dr. Yoo,

I just wanted to reiterate. I am going to create another dataset where there are going to be three columns per gene with the following names:

    GENENAME_EXP with three states (UP, DOWN, and everything else)

    GENENAME_AMP with two states (AMP;UP/DOWN; and everything else)

    GENENAME_MUT with two states (MUT/HOMDEL;UP/DOWN; and everything else)

If so, when I come back tomorrow, I'll set it up as such and run it.


It should be:

    GENENAME_EXP with three states (anywhere there is UP, anywhere there is DOWN, and everything else)

    GENENAME_AMP with two states (anywhere there is AMP and everything else)

    GENENAME_MUT with two states (anywhere there is MUT/HOMDEL and everything else)
cwyoo
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Re: Datasets

Postby meninonas » Wed Jan 28, 2015 6:58 pm

Empty
Last edited by meninonas on Tue Feb 03, 2015 2:24 pm, edited 3 times in total.
meninonas
 
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Re: Datasets

Postby cwyoo » Wed Jan 28, 2015 9:01 pm

meninonas wrote:Dr. Yoo,

I have worked on the dataset below. Tomorrow, I'll continue working on the dataset tomorrow.


Always use reference coding, i.e., in GENE_EXP you have 0, 1, 2 for "anywhere there is DOWN", "all others", "anywhere there is UP" respectively; in GENE_MUT, you have 0, 1 for "all others", "anywhere there is MUT" respectively; GENE_AMP, you have 0, 1 for "all others", "anywhere there is AMP" respectively.

Create three tabs for GENE_EXP, GENE_MUT, and GENE_AMP respectively.
cwyoo
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Re: Datasets

Postby cwyoo » Thu Jan 29, 2015 7:33 am

meninonas wrote:Dr. Yoo,

I installed Banjo on the Virtual Machine and on the computer and the following error was given to me:

Code: Select all
-----------------------------------------------------------------------------
(Final Checkpoint, after post-processing) A final check revealed the following issues that were encountered during Banjo's execution:
-----------------------------------------------------------------------------
(Post-processing) Postprocessing cannot proceed because we can't process the high score network(s).


I ran it on path4 and the following is the error that proceeds the above line:

Code: Select all
[ERROR: Banjo 2.2.0, 1/29/15 6:21:16 AM]
The following info is provided to assist in trouble-shooting:
The input line ' 89 0' in 'static.mandatory.str' is a repeat entry for variable '89'.



Stack trace info:

edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.loadStructureFile(EdgesAsArrayWithCachedStatistics.java:2862)
edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.<init>(EdgesAsArrayWithCachedStatistics.java:633)
edu.duke.cs.banjo.bayesnet.BayesNetManager.<init>(BayesNetManager.java:273)
edu.duke.cs.banjo.learner.SearcherSimAnneal.setupSearch(SearcherSimAnneal.java:1092)
edu.duke.cs.banjo.learner.SearcherSimAnneal.<init>(SearcherSimAnneal.java:723)
edu.duke.cs.banjo.application.BanjoThreadHandler.<init>(BanjoThreadHandler.java:115)
edu.duke.cs.banjo.application.Banjo.runMultipleInstances(Banjo.java:200)
edu.duke.cs.banjo.application.Banjo.execute(Banjo.java:150)
edu.duke.cs.banjo.application.Banjo.main(Banjo.java:447)

-----------------------------------------------------------------------------
                           End of error notification
-----------------------------------------------------------------------------
Error message while trying to record the error:
java.lang.NullPointerException


This is due to the setting that you have indicated that you are going to use:

Code: Select all
 mustBePresentEdgesFile =        static.mandatory.str


I have commented it out and it runs successfully in path4.

Code: Select all
## mustBePresentEdgesFile =        static.mandatory.str


However, we need to use above setting and the following setting in GENE_EXP, GENE_MUT, and GENE_AMP combined data:

Code: Select all
mustNotBePresentEdgesFile =


Please look into those options and learn how to specify the edges in the files.
cwyoo
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Re: Datasets

Postby meninonas » Fri Feb 06, 2015 6:01 pm

Dr. Yoo,

Please find 10 of the 11 datasets below. They are already coded and set up.
Attachments
Elf2 signaling.csv
(398.73 KiB) Downloaded 140 times
Estrogen Receptor Signaling.csv
(186.32 KiB) Downloaded 132 times
Mitochondrial Dysfunction.csv
(242.83 KiB) Downloaded 141 times
Mitotic polo-like kinases.csv
(146.77 KiB) Downloaded 151 times
Neurotrophin Signaling.csv
(141.07 KiB) Downloaded 134 times
Oxi Phospho.csv
(208.89 KiB) Downloaded 146 times
Parkinson.csv
(197.56 KiB) Downloaded 148 times
Remodeling of epith. adh junc.csv
(135.43 KiB) Downloaded 147 times
Spliceosome.csv
(220.1 KiB) Downloaded 143 times
transcriptional repression path.csv
(84.66 KiB) Downloaded 143 times
Last edited by meninonas on Mon Feb 09, 2015 3:29 pm, edited 2 times in total.
meninonas
 
Posts: 137
Joined: Tue Jun 24, 2014 3:25 pm
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