I am interested in using the pvclust R package to determine significance of clusters that I have generated using the regular hierarchical clustering hclust function in R. I have a datamatrix that consists of ~ 8000 genes and their expression values at 4 developmental time points. The code below shows what I use to perform regular hierarchical clustering on my data. My first question is: Is there a way to take hr.dendrogram plot and apply that to pvclust? Secondly, pvclust seems to cluster columns, and it seems more appropriate for data that is being compared across columns rather than rows like I want to do (I have seen many examples where pvclust is used to cluster samples rather than genes). Has anyone used pvclust in a similar fashion to what I want to do? My simple code for regular hierarchical clustering is as follows:
mydata<-read.table("Developmental.genes",header=TRUE, row.names=1)
mydata<-na.omit(mydata)
data.corr <-cor(t(mydata),method="pearson")
d<-as.dist(1-data.corr)
hr<-hclust(d,method="complete",members=NULL)
hr.dendrogram.<-plot(as.dendrogram(hr))
I appreciate any help with this!
