Question: WGCNA for less than 15 samples
gravatar for Bioinformatist Newbie
3.1 years ago by
Bioinformatist Newbie230 wrote:

In FAQ's of WGCNA package it's mentioned "We do not recommend attempting WGCNA on a data set consisting of fewer than 15 samples". What could be an alternate approach if one have let's say 6 samples? Can anybody explain if for example I want to analyze this gene expression data then from where will I start?

wgcna • 1.3k views
ADD COMMENTlink modified 3.1 years ago by Brian Gudenas90 • written 3.1 years ago by Bioinformatist Newbie230

What is your actual goal?

ADD REPLYlink written 3.1 years ago by Devon Ryan85k

Co-expression network analysis.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Bioinformatist Newbie230
gravatar for Brian Gudenas
3.1 years ago by
United States
Brian Gudenas90 wrote:

You can make an easy co-expression network by simply constructing the symmetric correlation matrix of all genes (adjaceny matrix as its called in WGCNA) then filtering that matrix by a hard threshold such as r = 0.70.

Although, based on your newest comment i am not sure why differential expression analysis is not sufficient. Couldn't they be ranked on highest absolute fold change or lowest FDR adjusted p-value?

ADD COMMENTlink written 3.1 years ago by Brian Gudenas90
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