0
$\begingroup$

I am trying to get the p-values for hierarchical clustering analysis on the following dataset.The dendrograms generated by pvclust and hclust are completely different.Because the pvclust mentioned they used the same method as hclust, it should be identical.

>test=read.delim("test1.txt", header=T)
> test

  S1 S2 S3 S4 S5 S6 S7 S8 S9 S10
1  1  1  1  1  1  1  0  1  1   0
2  0  0  1  0  0  0  0  0  0   0
3  1  0  0  1  1  0  0  0  1   1
4  1  0  1  0  1  1  0  1  0   1
5  0  1  0  1  0  0  0  0  1   0
6  1  0  1  0  1  1  0  0  0   1
7  1  1  0  1  0  0  1  0  1   0
8  1  1  0  1  0  1  1  0  1   0
9  1  0  1  0  1  1  0  1  0   0

> div.norm=decostand(test,"normalize")
> div.ch=vegdist(div.norm,"bray")
> div.ch.UPGMA=hclust(div.ch,method = "average")
> plot(div.ch.UPGMA)

This generates the following dendrogram: Dendrogram using hclust

Then I tried to run the same dataset using pvclust.

> test.tr=t(test)
> result=pvclust(test.tr, method.dist="cor", method.hclust="average", nboot=1000)
> plot(result)

I get the following dendrogram which is different from the one generated by hclust. Dendrogram using pvclust Some suggested that I should not transpose the data. But that produces a dendrogram where the columns are clustered (I don't want that).

Any help would be greatly appreciated!

$\endgroup$
  • $\begingroup$ The dendograms are almost identical. Why do you think they are completely different? $\endgroup$ – Peter Flom Aug 10 '16 at 13:11
  • $\begingroup$ @Peter: In this particular case of a small dataset, they are not very different. For other large datasets, they are quite different. Anyway, they should be identical and they are not. $\endgroup$ – user127213 Aug 10 '16 at 13:31
1
$\begingroup$

It's a bit late, but it seems that different distance calculation methods were applied to the 2 clustering algorithms.

You used "bray" in the 1st case, but "cor"(correlation) in the 2nd case.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.