What Tool/Package Would You Recommend For Clustering Large Gene Expression Data?

Question

[Diwan]

Hi All,

I have a large gene expression dataset of 10K genes with 800 conditions. This is after preprocessing/filtering. I am able to use many R hierarchical clustering tools using correlation/euclidean distance etc. I noticed that packages like pvclust does not work for such large dataset. There are also many other packages out there. Will it be worth to check each package and see if any cluster is identified using most of the methods ?

What package would you use/recommend to cluster large gene expression data?

Thanks Diwan

Answer 1

[Michael]

The amap package contains several clustering algorithms that should handle datasets of this size easily.

[Diwan]

Thanks Michael.

Answer 2

[vj]

If you are comfortable with R then you can try WGCNA

Answer 3

[5heikki]

What package would you use/recommend to cluster large gene expression data?

The same one(s) they use in high impact publications.

[Steve Lianoglou]

If you can't provide a helpful answer, why bother posting one at all?