Quick math will tell you that if we are looking for 10,000 SNPs and there are over 400,000 features on an array, that there are a lot more features than SNPs. That's because Affymetrix genotyping arrays essentially ask the same question — which SNP is at this particular location — in 40 different ways to make certain that the answer they get is correct. Each time we ask the question, we use a different probe, meaning that there are 40 different probe sequences used to decide the genotype of every SNP on the array. For a microarray that genotypes 10,000 or even 100,000 SNPs, you can quickly see how that adds up to millions and millions of probes.