MCODE and clustermaker2 problem

[dim hmmaros]

Hi all,

i have 2 initial networks that i want to analyze.

1)i run MCODE at each network separately with default options.

2)At each separately i run clusterMaker2->MCODE with default options and check two last options "Create new clustered network" and "Restore inter-cluster edges after layout" so i get two networks NET1 and NET2.

3)i run MCODE(*original) at NET1 and NET2.

RESULTS:

1)the clusters for both initial networks at steps 1 and 2 are exactly the same(obviously!!!)

The reason that i did this was because clusterMaker2 creates a new network differentiating the clusters. And running MCODE again for this network you can choose your cluster(from result Panel) and observe it.

Here i observed that while clusterMaker2 find the same clusters with MCODE it doesnt visualyze them right.

For one of my two initial networks the visualizations was wrong.I clicked on clusters of Result Panel and i saw sparsely nodes......

I dont know if i was clear enough.

Anyone know why this happened? 

[Scooter Morris]

Greetings!

I'm a little confused about what the issue is.  Are you saying that the clusterMaker2 Result Panel is showing the right clusters, but connecting them incorrectly to the network?  Do you have an example session file that shows the problem?  I'm happy to take a look at it.

-- scooter

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[dim hmmaros]

Hi again!

The problem maybe is that i take different results from clusterMaker2->MCODE and MCODE.Thats why the connection it incorectly.have the latest version of both.

I attach a session file with two networks. One of them has this problem...but why is this happening?

Τη Σάββατο, 7 Φεβρουαρίου 2015 - 9:02:38 μ.μ. UTC+2, ο χρήστης Scooter Morris έγραψε:

Greetings!

I'm a little confused about what the issue is.  Are you saying that the clusterMaker2 Result Panel is showing the right clusters, but connecting them incorrectly to the network?  Do you have an example session file that shows the problem?  I'm happy to take a look at it.

-- scooter

On 02/07/2015 03:12 AM, dim hmmaros wrote:

Hi all,

i have 2 initial networks that i want to analyze.

1)i run MCODE at each network separately with default options.

2)At each separately i run clusterMaker2->MCODE with default options and check two last options "Create new clustered network" and "Restore inter-cluster edges after layout" so i get two networks NET1 and NET2.

3)i run MCODE(*original) at NET1 and NET2.

RESULTS:

1)the clusters for both initial networks at steps 1 and 2 are exactly the same(obviously!!!)

The reason that i did this was because clusterMaker2 creates a new network differentiating the clusters. And running MCODE again for this network you can choose your cluster(from result Panel) and observe it.

Here i observed that while clusterMaker2 find the same clusters with MCODE it doesnt visualyze them right.

For one of my two initial networks the visualizations was wrong.I clicked on clusters of Result Panel and i saw sparsely nodes......

I dont know if i was clear enough.

Anyone know why this happened? 

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[Scooter Morris]

Hi there,
    Can you give clusterMaker2 0.9.5 a try?  I've made a bunch of fixes to the MCODE implementation to map more closely with the upstream code.

-- scooter

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[dim hmmaros]

Hello again...have you any idea for what is happening???

I would be happy if i knew anything about this...

Thank you!

Τη Σάββατο, 7 Φεβρουαρίου 2015 - 9:02:38 μ.μ. UTC+2, ο χρήστης Scooter Morris έγραψε:

Greetings!

I'm a little confused about what the issue is.  Are you saying that the clusterMaker2 Result Panel is showing the right clusters, but connecting them incorrectly to the network?  Do you have an example session file that shows the problem?  I'm happy to take a look at it.

-- scooter

On 02/07/2015 03:12 AM, dim hmmaros wrote:

Hi all,

i have 2 initial networks that i want to analyze.

1)i run MCODE at each network separately with default options.

2)At each separately i run clusterMaker2->MCODE with default options and check two last options "Create new clustered network" and "Restore inter-cluster edges after layout" so i get two networks NET1 and NET2.

3)i run MCODE(*original) at NET1 and NET2.

RESULTS:

1)the clusters for both initial networks at steps 1 and 2 are exactly the same(obviously!!!)

The reason that i did this was because clusterMaker2 creates a new network differentiating the clusters. And running MCODE again for this network you can choose your cluster(from result Panel) and observe it.

Here i observed that while clusterMaker2 find the same clusters with MCODE it doesnt visualyze them right.

For one of my two initial networks the visualizations was wrong.I clicked on clusters of Result Panel and i saw sparsely nodes......

I dont know if i was clear enough.

Anyone know why this happened? 

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[dim hmmaros]

Hi,
after this update all work fine...thank you a lot.This tool is so useful for me!!! :D