role of R value in co-expression network

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Elham Dallalbashi

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Jan 31, 2017, 4:56:31 PM1/31/17
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I am new in network and have a question,It may be a strange question!!
I calculate co-expression correlation by R and now I want to visualise it in Cytoscape, when we calculate correlation we filter genes per their r value, the value of r can has role in network? I mean it has role in Thickness of interaction for example?

Barry Demchak

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Jan 31, 2017, 4:57:44 PM1/31/17
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Sandeep Amberkar

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Feb 1, 2017, 10:02:23 AM2/1/17
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Hi Elham,

Edge weights in a network always have to be positive, you may need to add a constant to your correlation coefficient if you want to use them as edge weight. You can then use the edge attributes -> edge weight -> continuous mapping to visualise the gradient of your correlation coefficient. Hope that helps.

Best,
Sandeep

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Warm Regards,
Sandeep Amberkar



On 31 January 2017 at 21:16, Elham Dallalbashi <elhamdal...@gmail.com> wrote:
I am new in network and have a question,It may be a strange question!!
I calculate co-expression correlation by R and now I want to visualise it in Cytoscape, when we calculate correlation we filter genes per their r value, the value of r can has role in network? I mean it has role in Thickness of interaction for example?
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Barry Demchak

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Feb 1, 2017, 10:03:45 AM2/1/17
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Hi, all –

 

The Discuss forum has been closed and is now transferred to the HelpDesk forum. Please resume your comments on cytoscape...@googlegroups.com

 

Thanks.

 

From: cytoscap...@googlegroups.com [mailto:cytoscap...@googlegroups.com] On Behalf Of Sandeep Amberkar
Sent: Wednesday, February 01, 2017 3:53 AM
To: cytoscap...@googlegroups.com
Subject: Re: [Cytoscape-discuss] role of R value in co-expression network

 

Hi Elham,

 

Edge weights in a network always have to be positive, you may need to add a constant to your correlation coefficient if you want to use them as edge weight. You can then use the edge attributes -> edge weight -> continuous mapping to visualise the gradient of your correlation coefficient. Hope that helps.

 

Best,

Sandeep


--

Warm Regards,
Sandeep Amberkar

 

 

On 31 January 2017 at 21:16, Elham Dallalbashi <elhamdal...@gmail.com> wrote:

I am new in network and have a question,It may be a strange question!!
I calculate co-expression correlation by R and now I want to visualise it in Cytoscape, when we calculate correlation we filter genes per their r value, the value of r can has role in network? I mean it has role in Thickness of interaction for example?


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