Consensus tree or “bootstrap proportions” from multiple hclust objects

问题

I have a list of hclust objects resulting from slight variations in one variable (for calculating the distance matrix)

now I would like to make a consensus tree from this list.

Is there a generic package to do this? I am hacking my way through some code from maanova and it seems to work - but it's ugly and it needs a lot of hacking since I am not doing "normal" bootstrapping (it's chemical data).

/Palle Villesen, Denmark

c1_list <- seq(10,100,by=10)
c2 <- 30
e<- 1
mboot <- list()
for (i in 1: length(c1_list) ) {
   c1 <- c1_list[i]
   cat("Doing C1=",c1,"...")
   x <- hclust(custom_euclidean(t(log2(data[, all]+1)), c1,c2,e), method='average')
   cat("..done\n")
   mboot[[i]] <- x # To get hclust object back use mbot[[i]] to get i'th object
}

#### Now extract the robust groups from mboot...

回答1:

First, have a look at Allan Tucker's code for consensus clustering, related to his paper "Consensus Clustering and Functional Interpretation of Gene Expression Data".

Here are a few other pointers:

You mentioned that you're using the maanova package; this can build a consensus tree out of bootstrap cluster result with the consensus() function. Have you tried that?
The ape package is intended for phylogenetic tree analysis, so it's possibly not completely relevant, but you might look into it. There is an example using hclust on R-Help.
Similarly, the nem package, which is part of bioconductor has some examples.

回答2:

Hm, that sounds like a boosting approach applied to clustering, and a quick Google search reveals quite an existing literature on boosting clustering. Maybe that is a start?

As for R code, there are always the Task Views on Clustering and Machine Learning.

来源：https://stackoverflow.com/questions/1642119/consensus-tree-or-bootstrap-proportions-from-multiple-hclust-objects

标签

dendrogram

hclust