Cluster stability/robustness
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Hello, I have used hclust to cluster a large data of 10K genes and 800 conditions and got 150 clusters as output. How can I show that these clusters are stable? What are the common metrics or parameters that are used to show that we have got a stable/robust cluster? Is there any package that will do this? Your reply will be very helpful. Thank you for your time in advance. Thanks Rafi -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.
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@james-w-macdonald-5106
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Hi Rafi, How about the clusterStab package? Best, Jim On 1/16/2014 11:03 AM, Rafi [guest] wrote: > Hello, > > I have used hclust to cluster a large data of 10K genes and 800 conditions and got 150 clusters as output. > > How can I show that these clusters are stable? > > What are the common metrics or parameters that are used to show that we have got a stable/robust cluster? > > Is there any package that will do this? > > Your reply will be very helpful. Thank you for your time in advance. > > Thanks > Rafi > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_3.0.2 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi James, Thanks for your reply. My understanding is clusterStab takes an input of expression matrix of genes and conditions and then output number of clusters and stability of clusters using hclust. In my case, I have already used hclust with dynamictreecut to generate clusters. So I am curious to check the stability of these clusters from this process. Is there a way to do it? Thank you in advance. Rafi On Thu, Jan 16, 2014 at 11:07 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Rafi, > > How about the clusterStab package? > > Best, > > Jim > > > > On 1/16/2014 11:03 AM, Rafi [guest] wrote: > >> Hello, >> >> I have used hclust to cluster a large data of 10K genes and 800 >> conditions and got 150 clusters as output. >> >> How can I show that these clusters are stable? >> >> What are the common metrics or parameters that are used to show that we >> have got a stable/robust cluster? >> >> Is there any package that will do this? >> >> Your reply will be very helpful. Thank you for your time in advance. >> >> Thanks >> Rafi >> >> -- output of sessionInfo(): >> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United >> States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] tools_3.0.2 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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 >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]
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Hi Rafi, Well, hypothetically you could use the ideas behind clusterStab, but would have to insert dynamicTreeCut() for cutree() in the permutation step. You can see the underlying function by typing clusterStab:::do.clusterComp at an R prompt after loading the clusterStab package. It's there for you to play with if you want. However, I don't know if using a variable tree cutting approach will add additional instability to the result or not, so good luck! Best, Jim On Thursday, January 16, 2014 4:22:14 PM, rafi A wrote: > Hi James, > > Thanks for your reply. My understanding is clusterStab takes an input > of expression matrix of genes and conditions and then output number of > clusters and stability of clusters using hclust. > > In my case, I have already used hclust with dynamictreecut to generate > clusters. So I am curious to check the stability of these clusters > from this process. Is there a way to do it? > > Thank you in advance. > > Rafi > > > On Thu, Jan 16, 2014 at 11:07 AM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Rafi, > > How about the clusterStab package? > > Best, > > Jim > > > > On 1/16/2014 11:03 AM, Rafi [guest] wrote: > > Hello, > > I have used hclust to cluster a large data of 10K genes and > 800 conditions and got 150 clusters as output. > > How can I show that these clusters are stable? > > What are the common metrics or parameters that are used to > show that we have got a stable/robust cluster? > > Is there any package that will do this? > > Your reply will be very helpful. Thank you for your time in > advance. > > Thanks > Rafi > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > LC_CTYPE=English_United States.1252 > LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > loaded via a namespace (and not attached): > [1] tools_3.0.2 > > -- > Sent via the guest posting facility at bioconductor.org > <http: bioconductor.org="">. > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Rafi I?ve found the ?clue? package on CRAN very useful for similar questions. http://cran.r-project.org/web/packages/clue/index.html Best wishes Wolfgang Il giorno 16 Jan 2014, alle ore 17:03, Rafi [guest] <guest at="" bioconductor.org=""> ha scritto: > > Hello, > > I have used hclust to cluster a large data of 10K genes and 800 conditions and got 150 clusters as output. > > How can I show that these clusters are stable? > > What are the common metrics or parameters that are used to show that we have got a stable/robust cluster? > > Is there any package that will do this? > > Your reply will be very helpful. Thank you for your time in advance. > > Thanks > Rafi > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_3.0.2 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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