WGCNA, analysis on two data sets
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19 months ago
halehashki • 0

Hello, I have two healthy and cancer data sets and want to do WGCNA analysis. My goal is to detect the genes that are significant/different in these two data sets comparing to each other. My questions is should I follow the second part (II. Consensus analysis of female and male liver expression data) in this page: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/

Or the third tutorial also consider the traits in calculation? I didn't see anything related to traits identifying in Adjacency and TOM calculation. But gene significance calculation get the traits information. So I am confused how the traits information is been considered in analysis. I will be thankful if you advice me what is the best way to use WGCNA for two data sets analysis.

Thanks, Haleh

WGCNA multi traits • 577 views
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Entering edit mode
19 months ago

Please read question 1 of the FAQ: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html

TLDR: you don't have enough samples

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Thank you for your response. I think my question wasn't clear. I have more than 20 samples, having two conditions (HC vs Non-HC). My question is when I have data sets of two conditions, how to use WGCNA that consider the condition in correlation calculation. What I see, even in Male and Female liver example, they do the analysis separately and then get the consensus one. Here I am not looking for consensus, I am looking for differences.

I will be thankful is someone can help me out. Thanks

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Hello, how is everything? Have you had any opinions on this issue? If yes, you could share the information with me, because I am having the same problem.

Thank you

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