How to extract the subcluster based on PCC (pearson correlation coefficient) in Hierarchical Clustering ?

Question

[BioLite]

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")

[BioLite]

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?

Answer 1

[Kevin Blighe]

Take a look at my answers, here:

• A: extract dendrogram cluster from pheatmap
• A: How can I get the ordered names or new matrix according to cluster result?

You want to use:

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

Kevin