Hello folks, I'm hoping that you can help me understand some of the results I'm getting from WGCNA when it comes to visualising a network.
I have managed to extract my modules from the data set, and graphed them against their trait data, and now I'm looking to produce a visualisation of the gene network for each cluster, which was my original aim in using WGCNA. Unfortunately, I am having some problems with every network looking completely identical and symmetrical.
When I open my network file in VisAnt, I am always greeted by a perfect circle, with a line of equal strength connecting every node in the network. When I investigate the text output itself, it seems fine, example below, but there is absolutely minuscule variation in the connection strength, with almost every value being 0.40 to 0.42...
Hibch Ndufb3 0 M0039 0.402953581463721 Hibch Acadl 0 M0039 0.413293496510016 Hibch Sdhc 0 M0039 0.402266127071595 Hibch Ndufs2 0 M0039 0.412983888989828 Hibch Iars2 0 M0039 0.410319082165815 Hibch Atp5c1 0 M0039 0.399168115779561 Hibch Nfs1 0 M0039 0.401863940513408 Hibch Ndufb5 0 M0039 0.402559122972561 Hibch Etfdh 0 M0039 0.411821948607482 Hibch Gatb 0 M0039 0.405798431101945 Hibch Atp5f1 0 M0039 0.402543447219872 Hibch Hadh 0 M0039 0.410937281224753 Hibch Cpt2 0 M0039 0.411218531292222 Hibch Atp5k 0 M0039 0.408706798256598 Hibch Mdh2 0 M0039 0.410767514376832 Hibch Adipor2 0 M0039 0.40568057005744
The list goes on like this, with the gene on the left hand cycling through my "top" hub genes, but the final value never exceeding 0.43 and never appearing lower than 0.38. I have even run through the export function with every single gene in the cluster (Just under 2000), and no single connection has a value outside of this range.
Is there some easy problem that I'm missing? I am simply using the "exportNetworkToVisAnt()" function as provided by the WGCNA package. Is the problem that none of my modules actually exhibit a single gene network?
Any help is greatly appreciated. Thanks in advance.