In WGCNA R package how do you correlate identified co-expression modules with binary phenotype data ? All the papers and tutorial material I have seen works with quantitative data. Does psuedo numbering traits ( 1 for control and 2 for disease sample) make any sense or are there any other options ?
In another case, i have different tissue, the information all I have is that these samples are from different tissue. How do I apply these data to WGCNA?