In WGCNA_stage4.R you will generate tables with correlation of modules and genes to each treatment. These tables will help you find genes that are interesting (correlate highly with treatments) even if they're not differentially expressed.

Prepare WGCNA_stage4.R script

Preparation of the WGCNA_stage4.R script is a little bit more elaborate than for the other stages. You will need to go through the entire script and make adjustments based on how many samples (RNAseq libraries) and treatments you have.

Output

All output will be stored in your "Data" directory.

"_eigengene-treatment.txt" contains all Module-Eigengenes' correlation values with each treatment.

"Module-treatment_cor.txt" contains the correlation of the modules with each treatment.

"Combined_gene-treatment_cor.txt" contains the correlation of each gene with each treatment.

"geneModuleMemebership.txt" contains the module membership scores for each gene.

"_Top_10_ModuleMembership_genes.txt" contains the top10 gene names for each module.

"Module_top1_HUB-genes.txt" shows the most connected gene in each module.