Question: WGCNA for less than 15 samples
1
gravatar for Bioinformatist Newbie
3.1 years ago by
Germany
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
0
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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1873 users visited in the last hour