WGCNA, the same network type in pickSoftThreshold and TOMsimilarity
Hi All,
I've started consensus WGCNA analysis for RNA-seq data.
The commands have many options and I've read appropriate section of the FAQ.
As it is not stated clearly I'd like to ask:
Does using networkType = "signed" in pickSoftThreshold implies that all other functions must be run with signed option?
For example:
I'm currently at the TOMsimilarity function level. It has TOMType option with choice: "none", "unsigned", "signed", "signed Nowick", "unsigned 2", "signed 2" and "signed Nowick 2".
There are more values than in pickSoftThreshold so I guess it is not the same.
Could someone clarify that, please.
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A note if someone would be interested in this post. So, ok, after extended research I've found that
TOMtypeandnetworkTypeare different:TOMtypeis different thannetworkType, so usingnetworkType = "signed"does not imply usingTOMtype = "signed"bioconductor postAnd more details on
TOMtypePeter Langfelder website