Hello, the overwhelming (i.e., >95%) majority of my bioinformatics experience is with the mitochondrial genome within my population of interest. As of last week, I have a SNP data from an Affymetrix Axiom Human Origins array (~629,000 SNPs) on a collection of my samples, and I am feeling absolutely overwhelmed. The first analysis I need to run on the data is to run a Principle Component Analysis to compare my samples to previously published populations (i.e., HapMap, HGDP, whatever else there is out there; all of which I still need to download).
I've got my data out of Genotyping Console; however, the format is a mess, for whatever reason a few thousand of the SNPs only have Affy IDs and not dbSNP rs ids, and I am not sure what I am doing (and unfortunately most of literature only describes what was done, never how it was done). I was wondering, can anyone point me in the direction of some form of tutorial on how to get my data into a principle component analysis? Thanks!