Question: How to extract the subcluster based on PCC (pearson correlation coefficient) in Hierarchical Clustering ?
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gravatar for BioLite
18 months ago by
BioLite20
BioLite20 wrote:

Hi, company, I am doing a Hierarchical Clustering with a gene expression data based on PCC (Pearson correlation coefficient), and want to extract the subcluster whose sum of PCC is the highest, I know cutree() can help me extract subgroup, however, how to output the highest PCC group? Any ideas? Thank you very much! BTW, here is my cluster code:

hc_w2=hclust(as.dist( 1-cor(t(clu_w2),method = "pearson")),method = "complete")
ADD COMMENTlink modified 18 months ago by Kevin Blighe56k • written 18 months ago by BioLite20

Maybe I can use cutree() extract every subgroup, and then calculate their PCC summations then making a comparison? But this doesn't like the best method?

ADD REPLYlink written 18 months ago by BioLite20
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gravatar for Kevin Blighe
18 months ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

Take a look at my answers, here:

You want to use:

cutree(MyTree, h=0.7) # cut at height 0.7

Kevin

ADD COMMENTlink modified 18 months ago • written 18 months ago by Kevin Blighe56k
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