Module sample correlation analysis in WGCNA

Question

[alim.hcu]

Dear All

I am doing WGCNA analysis of different tissue samples from a plant. After Module identification, I want to calculate module sample relationship analysis. For module and sample correlation, we have to use two different values one from module and another from samples. For module we can use expression of each module. But for samples, what type of data we will use for sample (leaf, root, stem, flower, sepal, petals).

Thank You

Answer 1

[Kevin Blighe]

The idea is to correlate or regress your phenotypes against the WGCNA modules. You can use anything that you want. If, for example, leaf is statistically significantly correlated to the pink module, then you would hypothesise that the genes in the pink module are related somehow to leaf

WGCNA is quite flexible and gives you, the user, much freedom to perform any analysis(es) that you please.

Kevin