Question: scale free topology in WGCNA
0
gravatar for mrashad
7 weeks ago by
mrashad50
mrashad50 wrote:

Dear this image resulted from plotting the result of picksoftthreshold function in WGCNA ![scale_free and mean connectivity][1] I need to ask what is the meaning of the sft result from using picksoftthreshold function in WGCNA as this result is considered as a list contain powerestimate which equal to 18 in my case and fitindices dataframe that contain 7 columns [ power, SFT.R.sq,slope,truncated.R.sq,mean.k.,median.k.,max.k.]. First: I just need to understand this dataframe and how power 18 is decided to be a power of my data. Second: What is the importance of mean connectivity plot ?, has it a role in determination of power ?. Third: what is the difference between networktype and TOMtype in blockwiseModules function?.

Note: that my data is expression of multiomics data contain 153 samples and 924 genes.

[1] https://i.ibb.co/qrwq1pn/scale-free-topology.png

#wgcna #network_analysis • 183 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by mrashad50

Honestly, it is the first time for me to use WGCNA and I used this tutorial as a guide: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-auto.pdf + video for its author:

but there is no step mention adjacency matrix, if there is another tutorial use adjacency I will be grateful to send me it.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by mrashad50
1

because that is the automatic one-step network construction tutorial. Instead, look at the step-by-step tutorial if you want to understand how wgcna works. Here the description of the blockwiseModules function

ADD REPLYlink written 7 weeks ago by andres.firrincieli1.1k
1
gravatar for andres.firrincieli
7 weeks ago by
andres.firrincieli1.1k wrote:

Hello,

153 samples and power of 18 for an unsigned network is too high. There is a very nice explanation about power selection here and here. In your case I would pick 9.

Third: what is the difference between networktype and TOMtype in blockwiseModules function?.

To construct a network in WGCNA you will need an adjacency matrix which is then converted in a topological overlap matrix (TOM). The argument networkType is used for the adjacency matrix while TOMtype is for the TOM. Since you have only 924 genes, there is really no need to use the blockwiseModules function, unless you are working with a laptop with 4 Gb of RAM.

ADD COMMENTlink written 7 weeks ago by andres.firrincieli1.1k
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