Question: how to filter genes in significant module?
0
gravatar for modarzi
10 days ago by
modarzi80
modarzi80 wrote:

Hi,

I used WGCNA for finding modules. I found 9 modules: turquoise(1501), red(173), pink(41), magenta(36), grey(6), green(446), brown(348), blue(382),black(67). Based on Univariate Cox Model just turquoise is significance. The number of 1501 genes in turquoise module is high and I have to filter more for Gene Enrichment Analysis (GEA) and finding significant pathway. So, how can I decrease the number of genes in turquoise module? Generally, is it reasonable that I run a new clustering into turquoise module?

I appreciate if anybody shares his/her comment with me.

significant modules wgcna • 90 views
ADD COMMENTlink written 10 days ago by modarzi80

Why do you need to reduce the number of genes? Did you pre-filter your data prior to performing WGCNA? Can you modify the tree cut height in order to reduce the size of this turquoise module?

Generally, is it reasonable that I run a new clustering into turquoise module?

You can do whatever you please - this is research. Try to think through what it may mean when you do this, though.

ADD REPLYlink modified 10 days ago • written 10 days ago by Kevin Blighe45k

Hi, my origin number of genes in the dataset is 3000 and after constructing, I find 9 modules as I said in the privous comment. The 1501 genes are high in a turquoise module. I would like to achieve a fewer number of genes for finding better results. I use cutreeDynamic() for Module identification based on the below code:

dynamicMods = cutreeDynamic(dendro = geneTree, distM = dissTOM,
                            deepSplit = 2, pamRespectsDendro = FALSE,
                            minClusterSize = 30);

As you see, in that function I have no choice for cutting height and the value of that is calculated automatically.

Now, do you have any more comment for reducing the

ADD REPLYlink written 10 days ago by modarzi80

Try deepSplit = 4

ADD REPLYlink written 10 days ago by Kevin Blighe45k
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