The Supplementary Material in pdf format can be downloaded here.

Here is the source code used to compute and visualize the stability of all clusters of a hierarchical clustering, as described in the paper.

To use this code:

- download the stability.c and stability.R files
- compile file
`stability.c`

with R:R CMD SHLIB stability.c

This produces the library

`stability.so`

- run R and load the
`stability.so`

library and the R programsdyn.load("stability.so") source("stability.R")

- Below is a small example of use with the wood datasource:
# Load the wood file that contains the array.bois object load("Wood.RData") ## Run a hierarchical clustering and compute the stability of every cluster ## array.dat is an array object: rows are genes/proteins, columns are ## biological conditions and depth correspond to experimental repetitions ## iterhc: number of samplings for the bootstrap procedure reswood<-validTree(array.dat=array.bois,iterhc=10) ## Compute the node stabilities by averaging on the different samplings stabwood<-apply(reswood$stab,2,mean) ## plot the dendrogram with the stabilities. ## minstab indicates the threshold stability. Only stabilities above this threshold are plotted. ## minmembers indicates the threshold of size clusters. Only stabilities of clusters above this threshold are plotted. dend <- decoreDendo(hc=reswood$hc,stab=stabwood,minstab=0.8,minmembers=5) plot(dend,leaflab="none",cex.axis=1.8)

brehelin at lirmm.fr