Question: How to extract the subcluster based on PCC (pearson correlation coefficient) in Hierarchical Clustering ?
0
gravatar for BioLite
14 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 14 months ago by Kevin Blighe52k • written 14 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 14 months ago by BioLite20
0
gravatar for Kevin Blighe
14 months ago by
Kevin Blighe52k
Kevin Blighe52k 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 14 months ago • written 14 months ago by Kevin Blighe52k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1781 users visited in the last hour