search

xiaolw95 / NetMoss2

Other
8 stars 4 forks source link

Setting soft_pow #9

Open juyanmei opened 2 years ago

juyanmei commented 2 years ago

Could you gave me some suggestions about setting soft_pow?

juyanmei commented 2 years ago

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 commented 1 year ago

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.