Question

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

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11.1 years ago

Diwan ▴ 650

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

expression clustering • 3.7k views

ADD COMMENT • link updated 11.1 years ago by vj ▴ 520 • written 11.1 years ago by Diwan ▴ 650

score 2 · Answer 1 · 2013-12-02

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11.1 years ago

Michael 55k

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

ADD COMMENT • link 11.1 years ago by Michael 55k

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Thanks Michael.

ADD REPLY • link 11.1 years ago by Diwan ▴ 650

score 1 · Answer 2 · 2013-12-04

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11.1 years ago

vj ▴ 520

If you are comfortable with R then you can try WGCNA

ADD COMMENT • link 11.1 years ago by vj ▴ 520

score 0 · Answer 3 · 2013-12-02

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11.1 years ago

5heikki 11k

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

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

ADD COMMENT • link 11.1 years ago by 5heikki 11k

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

ADD REPLY • link 11.1 years ago by Steve Lianoglou 5.2k