Dear all:
I am trying to run WGCNA on my RNA-seq dataset (20 samples, 2 conditions 10 obs each). I had a batch effect corrected with edgeR.
When I try to apply the soft threshold on my dataset I run into the following dilemma: if I set the network type "unsigned" I obtain a soft threshold of 15. If I rather make it "signed" then even after a power of 30 it doesn't get a scale free topology index of 0.9.
My knowledge in statistics is limited, and I cannot understand the reasons for such a weird behavior.
Can anyone help?
Thanks!
Manu
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written
by
emanuela.molinari •
1 answer
A scale free topology index of 0.9 or greater is not required for WGCNA, although it should probably be above 0.8
Just take a look at the R code from this publication (authored by the creator of WGCNA), they use a soft threshold of 26 (signed network) which only achieves an index of 0.808.
http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/developingcortex/
It sounds like the issue is in the connectivity of your RNA-seq data though, is it being filtering by some criteria such as differential expression?
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written
by
Brian Gudenas
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