role of R value in co-expression network

[Elham Dallalbashi]

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]

... Moving this to cytoscape...@googlegroups.com ...

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[Sandeep Amberkar]

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]

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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You received this message because you are subscribed to the Google Groups "cytoscape-discuss" group.

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-disc...@googlegroups.com.
To post to this group, send email to cytoscap...@googlegroups.com.

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