Question: Hierarchical Clustering-Dendrogram Cut-Off
1
gravatar for Diana
7.9 years ago by
Diana800
Germany
Diana800 wrote:

I have microarray data and I want to identify groups of genes that have same expression patterns across my samples. I've done average linkage hierarchical clustering in R. How can I detect which cut-off would be best for dendrogram so I have significant clusters? The height (combination similarity) of my dendrogram goes from 0 to about 2.5 with almost all clusters of genes between the height of 0 and 0.5. How important is it to have a cut-off?

Many thanks.

clustering • 6.0k views
ADD COMMENTlink modified 6.4 years ago by Biostar ♦♦ 20 • written 7.9 years ago by Diana800

watch here : http://biostar.stackexchange.com/questions/699/

ADD REPLYlink written 7.9 years ago by toni2.1k
4
gravatar for John
7.9 years ago by
John1.5k
John1.5k wrote:

It is slighly different approach, but is useful to do bootstrap to see stablitity of the clusters. You can use R package Pvclust.

library (pvclust)

result < - pvclust(data, nboot=10000)

plot(results)

ADD COMMENTlink written 7.9 years ago by John1.5k

pvclust is pretty sweet!

ADD REPLYlink written 7.9 years ago by Zev.Kronenberg11k
0
gravatar for Vitis
7.9 years ago by
Vitis2.3k
New York
Vitis2.3k wrote:

This is a very hard decision to make. First, you can plot the within group sum of squares along the number of clusters to find the optimum number then cut the tree (dendrogram) accordingly. Then, there are very sophisticated dynamic tree cutting approaches being developed, for example: http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/ These methods are more involved so you may need to read more about them.

ADD COMMENTlink written 7.9 years ago by Vitis2.3k
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