Hello,
I am trying to perform a WGCNA with microarray expression data, but I haven't perform it before. The samples are iPS-derived neural progenitors from two genetic conditions (WBS - Williams-Beuren syndrome patients and DUP7 - microduplication 7q11.23 patients) and controls. Therefore, once I have identified the modules, I would like to study the association with the trait of interest, that in this case is the gene dosage in 7q11.23 imbalances... so, it is a quantitative trait. Individuals with Williams have a microdeletion in 7q11.23 (1 copy), DUP7 patients have a microduplication at 7q11.23 (3 copies) and controls are diploid (two copies). This is why, I thought the best way to represent that was coding the condition by the number of copies: 1 - deletion (WBS), 2 - controls, and 3 - duplication (DUP7). Am I doing it right?
I don't know if it would be better to separate the traits in deletion and duplication. So, on the one hand, one trait would be the deletion where WBS patients would have a 0, and the rest a 1; On the other hand, the second trait would be the duplication, where DUP7 patients would have a 0 and the rest a 1 (or vice versa).
If someone could give a hand, I would really appreciate it!
Thanks in advance, and happy new year!