Question: Automatic clustering for gene expressing matrix
0
gravatar for J.F.Jiang
4.6 years ago by
J.F.Jiang750
China
J.F.Jiang750 wrote:

Hi all,

I am dealing with the co-expression modules using WGCNA.

WGCNA is highly recommend for its softhresholding and preservation analysis of the expression data.

The method can automaticly generate some modules (networks) in co-expression manner.

Basically, the co-expression modules can be obtained as followed,

1) calculate the pearson correlation of the expression matrix

2) set a predefined cutoff (e.g., 0.8~0.9) to obtain those highly connected edges

3) apply k-means, SOM... clustering method to obtain the modules,

However, these clustering method required a given number for the expected clusters.

I am wondering if there is any tool that can take the expression matrix as input, and automatically obtain the co-expression modules?

Best

 

ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 4.6 years ago by J.F.Jiang750

Maybe this tool can help you http://bonsai.hgc.jp/~mdehoon/software/cluster/

ADD REPLYlink written 4.6 years ago by roy.granit790

Thanks, the method in the web you offered is a combination of several popular methods, such as kmeans,hclust, and so on.

What I mean is to find a tool that can handle expression matrix as input just as WGCNA.

Thank, if there is no one, I will write the script.

ADD REPLYlink written 4.6 years ago by J.F.Jiang750

But why can't you use WGCNA?

ADD REPLYlink written 4.6 years ago by PoGibas4.8k

I just want to compare the outputs of them.

ADD REPLYlink written 4.6 years ago by J.F.Jiang750

Does WGCNA (blockwiseModules) require number of modules?

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by PoGibas4.8k
1

WGCNA will not require the input of module number, so it is "automatic".

 

ADD REPLYlink written 4.6 years ago by J.F.Jiang750
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