how to use singular value detection for identification of modules in wgcna

Question

[rajasekargutha]

i am using WGCNA and identified 12modules for 6 traits. to further understand the relation between modules and traits some papers mentioned singular value detection for identification . can any one help me how to perform for my data modules. i have followed WGCNA tutorials but I couldn't understand to proceed further. in this paper https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-2-16 they used for module selection.

Answer 1

[Jean-Karim Heriche]

Have you looked at the relevant references from the paper you linked to, in particular Alter et al. ?
It is simply a matter of applying SVD to the genes x conditions matrix. Figure 7 of Alter et al. should help you interpret the result.

[rajasekargutha]

could you explain little moare as i am new to this work, and if possible post r code for performing SVD. I have identified 12 modules for 6 traits and i want to see the relation between modules and traits.

[rajasekargutha]

could you explain little moare as i am new to this work, and if possible post r code for performing SVD. I have identified 12 modules for 6 traits and i want to see the relation between modules and traits.