I am working on a meta-analysis in which I am trying to find differential gene expression across pain conditions and compare their fold changes. My PI told me that I cannot use GWAS studies because somehow the results are not comparable to those of PCR, RNA-seq, and western blots. I don't understand why this is. Can anyone help me differentiate between GWAS results and results from other assays?
That's a good question. My understanding of the issues are the GWAS are often taken from a small number of primers that are chosen for whatever reason, so significance essentially says "variants in this chromosome in the population are associated with the disease". Essentially GWAS may give you information that an inherited chromosome is associated with the disease while RNA-seq gives you much greater resolution (the actual coding variant, if that is what caused the disease).
I'm not sure how Western Blots would tie into this. Maybe you misunderstood your PI?