How To Assess Dendrogram Robustness

Question

[Julien Textoris]

Hi all,

I would like to assess the robustness of a dendrogram.

The general purpose is to compare biological samples evaluated by mass spectrometry. I developped an algorithm in order to compute a distance matrix in order to classify samples. I would like to assess the robustness of the obtained dendrogram, but i don't know really how to do so. I knew that a bioconductor package called pvclust was able to do so by bootstrapping, the problem is taht pvclust function does not accept a user-defined distance matrix computation function.

Do you know either

• if there is another package which would allow me to define my distance definition (or distance matrix computation function)
• if there are a good introductory course on clustering / dendrogram robustness assessment ?

Thanks in advance,

Julien

Answer 1

[Darren J. Fitzpatrick]

The authors of pvclust provide a method whereby you can call a custom distance function. It involves you defining your distance function in R and then setting the method.dist argument equal to your function.

http://www.is.titech.ac.jp/~shimo/prog/pvclust/pvclustunofficial090824/readme.txt

[Julien Textoris]

Thank you very much, that's just what i needed !

Julien