[BioC] Cluster stability/robustness

James W. MacDonald jmacdon at uw.edu
Thu Jan 16 23:24:35 CET 2014


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>.
>
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>
>     --
>     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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