Utility of WGCNA with minimal samples?

[aspencoyle]

Hi all!

I'm working my way through the tutorials for running WGCNA, and noticed that within the FAQ, they state "We do not recommend attempting WGCNA on a data set consisting of fewer than 15 samples"

I'm not even close to this - each of my pairwise comparisons has 6 total samples (3 per treatment group), which is...well under the recommended total!

Should I increase sample size by pooling similar treatments together (for instance, pooling Ambient Day 0 and Ambient Day 2)?

Should I keep my groups as is and run WGCNA despite its limitations with a limited sample size?

Or should I just look for another tool for this particular job?

[sr320]

Run with what you have.

On Thu, Mar 18, 2021 at 6:05 PM afcoyle ***@***.***> wrote: Hi all! I'm working my way through the tutorials for running WGCNA, and noticed that within the FAQ <https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html>, they state "We do not recommend attempting WGCNA on a data set consisting of fewer than 15 samples" I'm not even close to this - each of my pairwise comparisons has 6 total samples (3 per treatment group), which is...well under the recommended total! Should I increase sample size by pooling similar treatments together (for instance, pooling Ambient Day 0 and Ambient Day 2)? Should I keep my groups as is and run WGCNA despite its limitations with a limited sample size? Or should I just look for another tool for this particular job? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1156>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABB4PN3CTZDBCEMVY6WJFOTTEKPI5ANCNFSM4ZNZUI4A> .

-- Steven B. Roberts, Associate Professor Associate Director - Graduate Program Coordinator School of Aquatic and Fishery Sciences University of Washington Fisheries Teaching and Research (FTR) Building - Office 232 1140 NE Boat Street - Seattle, WA 98105 robertslab.info - ***@***.*** - @sr320 vm:206.866.5141 - cell:360.362.3626

[aspencoyle]

Thanks Steven, will do!

For anyone in the future reading this, I found this guide to WGCNA really helpful with some of the basic principles - wish I'd checked it out before diving into the tutorials

[sr320]

Big picture is we want to see expression clusters (based on temporal patterns) in individual crabs over time

On Thu, Mar 18, 2021 at 6:37 PM afcoyle ***@***.***> wrote: Thanks Steven, will do! For anyone in the future reading this, I found this guide to WGCNA <https://edu.isb-sib.ch/pluginfile.php/158/course/section/65/_01_SIB2016_wgcna.pdf> really helpful with some of the basic principles - wish I'd checked it out before diving into the tutorials — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1156 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABB4PN2A7IFWB5CMALID5KDTEKTE7ANCNFSM4ZNZUI4A> .

-- Steven B. Roberts, Associate Professor Associate Director - Graduate Program Coordinator School of Aquatic and Fishery Sciences University of Washington Fisheries Teaching and Research (FTR) Building - Office 232 1140 NE Boat Street - Seattle, WA 98105 robertslab.info - ***@***.*** - @sr320 vm:206.866.5141 - cell:360.362.3626