[BioC] Cluster stability/robustness

[James W. MacDonald]

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