Question: Testing for significant clustering in dendrograms of gene expression
0
gravatar for 4galaxy77
2.8 years ago by
4galaxy7760
United Kingdom
4galaxy7760 wrote:

I am looking for some help on a statistical test I could use on my dendrogram of gene expression. I have used the dendrogram/heatmap function in pheatmap to produce this, to see whether my samples cluster in any particular pattern. Obviously you can visually inspect the figure, but I would like something a bit more rigorous.

http://i66.tinypic.com/2r6ip14.jpg

For example, it might be that the alpha individuals cluster together more than would be expected by chance (although it clearly looks as though this isn't the case). Can anyone recommend a program (perhaps an R package) which could implement a test of this nature? Thanks.

rna-seq • 1.2k views
ADD COMMENTlink modified 2.8 years ago by Jean-Karim Heriche21k • written 2.8 years ago by 4galaxy7760
2

Have a look at pvclust in R. It performs a multiscale bootstrap analysis of clusters from hierarchical clustering methods. https://cran.r-project.org/web/packages/pvclust/index.html

ADD REPLYlink written 2.8 years ago by ejm32440

Ah that looks perfect, thanks!

ADD REPLYlink written 2.8 years ago by 4galaxy7760

pvclust gives you an idea of how strongly the data support the clustering but this won't tell you if alphas cluster together more than expected by chance.

ADD REPLYlink written 2.8 years ago by Jean-Karim Heriche21k

Hierarchical clustering is also called unsupervised clustering, hence without prior knowledge. If you want to test if alpha is different from beta, you should use something like limma to find differentially expressed (DE) genes between the groups. If you'll cluster then with the DE genes only you'll probably get better heatmaps.

ADD REPLYlink written 2.8 years ago by Benn7.9k
1
gravatar for Jean-Karim Heriche
2.8 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

You could try adapting the CLEAN (CLustering Enrichment ANalysis) method. An alternative would be to make disjoint clusters and test whether they are enriched in a particular type compared to the population.

ADD COMMENTlink written 2.8 years ago by Jean-Karim Heriche21k

thank you for your help. i will have a look at this.

ADD REPLYlink written 2.8 years ago by 4galaxy7760
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