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Setting soft_pow #9

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juyanmei opened this issue Jul 4, 2022 · 2 comments
Open

Setting soft_pow #9

juyanmei opened this issue Jul 4, 2022 · 2 comments

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@juyanmei
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juyanmei commented Jul 4, 2022

Could you gave me some suggestions about setting soft_pow?
@juyanmei
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juyanmei commented Jul 4, 2022

Can I use these codes to choose the appropriate soft_pow?
What if the soft_pow is different between the case network and the control network? Should I just choose it based on the number of samples following WGCNA https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/faq.html?
powers = c(c(1:10), seq(from = 12, to = 30, by = 2))
adj <- as.matrix(0.5 + 0.5 * network)
soft = pickSoftThreshold(adj, dataIsExpr = F, powerVector = powers, RsquaredCut = 0.85)

@xiaolw95
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Your codes are ok for the determination of soft_pow but I am afraid that the current version of NetMoss does not work for different parameters of case-control groups. I will improve it in the next version. Thanks anyway.

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