WGCNA chooseTopHubInEachModule function
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@sudeep-sahadevan-5349
Last seen 8.4 years ago
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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Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 2.4 years ago
United States
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@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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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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@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. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- A model is a lie that helps you see the truth. Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> ________________________________ IMPORTANT WARNING: This email (and any attachments) is o...{{dropped:9}}
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@sudeep-sahadevan-5349
Last seen 8.4 years ago
Dear Steve, Thank you for your reply (and thanks to Tim for forwarding the mail) Regards, Sudeep. ----- Original Message ----- From: "Steve Horvath" <shorvath@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@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. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- A model is a lie that helps you see the truth. Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> ________________________________ IMPORTANT WARNING: This email (and any attachments) is o...{{dropped:2}}
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