I recently got back some genotyping data back from the core lab from the Axiom Human Orgins array, and I have been trying to analyze it (trying being the operative word). I have been having some major frustrations.
I was trying to run a PCA in R when I noticed that a few thousand of the rows were pairs sharing the same rs ID. (In case it is relevant, the table was constructed with rs IDs making up the rows with each column being a sample genotype coded as 0/1/2). I noticed this was the case within Genotyping console also (as well as when I export data out of it). There are many cases where there are two Probe Set IDs for the same Affy SNP ID and dbSNP RS ID values...
Anyone know why is this? Is this indicative of the exact same site being genotyped twice? How do I filter these cases out, so that when I export genotypes I am not getting duplicates of the same loci? Thanks!