Question: What Tool/Package Would You Recommend For Clustering Large Gene Expression Data?
1
gravatar for Diwan
6.2 years ago by
Diwan570
United States
Diwan570 wrote:

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 • 2.4k views
ADD COMMENTlink modified 6.2 years ago by vj420 • written 6.2 years ago by Diwan570
2
gravatar for Michael Dondrup
6.2 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

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

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Michael Dondrup47k

Thanks Michael.

ADD REPLYlink written 6.2 years ago by Diwan570
1
gravatar for vj
6.2 years ago by
vj420
UK
vj420 wrote:

If you are comfortable with R then you can try WGCNA

ADD COMMENTlink written 6.2 years ago by vj420
0
gravatar for 5heikki
6.2 years ago by
5heikki8.6k
Finland
5heikki8.6k wrote:

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

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

ADD COMMENTlink written 6.2 years ago by 5heikki8.6k
8

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

ADD REPLYlink written 6.2 years ago by Steve Lianoglou5.0k
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