I have got .dat and .cell from Affymetrix 2.0 platform. It's a Custom Array-based genotyping experiment, it is designed to perform deep replication to establish disease signals and fine mapping of GWAS loci. Now my Question is how to perform an analysis so that the highly frequent genes and their respective SNPs related to a Disease can be found. It would be really helpful if you can share the analysis steps/pipeline involved or any other tutorials in this respect.
Thanks a lot for your kind help,
P.S: I have around 2000 samples (Disease and normal)