Hi, I am working on plant microarray data in drought condition. I am using WGCNA (R package) for building co-expression modules. In the tutorial, they have mentioned about clinical trait data. I wanted to know what kind of data I can use in my case ? fold change ?..any suggestions will be very much appreciated.
WGCNA is used to create clusters of gene (modules) that are co-expressed among your samples and then to correlate the modules with a trait/condition to find groups of genes that seem to vary in expression with changes in your trait/condition. Finding the co-expression of your modules with fold-change is a strange idea.
I am not sure what this would tell you. You would be trying to find gene modules that vary in expression. I suppose you probably already have a statistical way of finding differently expressed genes from your data.
If I remember well, I think you can use discreet traits, so you could try to correlate with drought condition (drought, no-drought). You can test multiple traits, so even better would be if you had different traits to test. For example: percent of leaves area that is dried (necrosed), millimetres of rain per day, number of days without water, etc.