[BioC] WGCNA chooseTopHubInEachModule function

[Sudeep Sahadevan]

Dear Steve,

Thank you for your reply

(and thanks to Tim for forwarding the mail)

Regards,
Sudeep. 

----- Original Message -----
From: "Steve Horvath" <SHorvath at mednet.ucla.edu>
To: ttriche at usc.edu, "Sudeep Sahadevan" <sudeep.sahadevan at scai-extern.fraunhofer.de>
Cc: bioconductor at r-project.org, "Peter Langfelder" <Peter.Langfelder at gmail.com>
Sent: Wednesday, June 20, 2012 6:19:52 PM
Subject: RE: [BioC] WGCNA chooseTopHubInEachModule function

Dear Tim and Sudeep,

regarding your question one can invoke a general rule linking unsigned and signed networks: if a power of beta is chosen for an unsigned network then one should choose a power of 2*beta for corresponding signed network.
Therefore, I suggest to use a power of 4 for a signed network.
In any event, the good news is that weighted networks are fairly robust with respect to (soft) threshold choices (i.e. the power) so the result should be fairly robust irrespective of the choice of beta.
Steve

________________________________
From: Tim Triche, Jr. [tim.triche at gmail.com]
Sent: Wednesday, June 20, 2012 6:38 AM
To: Sudeep Sahadevan
Cc: bioconductor at r-project.org; Horvath, Steve; Peter.Langfelder at gmail.com
Subject: Re: [BioC] WGCNA chooseTopHubInEachModule function

WGCNA is not a BioC package, you should cc: the authors (Steve Horvath and Peter Langfelder) on your email (IMHO)


On Wed, Jun 20, 2012 at 2:36 AM, Sudeep Sahadevan <sudeep.sahadevan at scai-extern.fraunhofer.de<mailto:sudeep.sahadevan at scai-extern.fraunhofer.de>> wrote:
Hi all,

In WGCNA R package the default "power" argument for the function "chooseTopHubInEachModule" is 2. My question is there anyway to test what would be the optimum argument to use for a signed network ?

Thank you in advance.

Regards,
Sudeep.

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