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.
>>
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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
>
>

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