In general, Affymetrix chips have more redundancy than do Illumina chips, in the sense of containing sets of SNPs which are correlated with each other. The immediate consequence of this is lower coverage and lower power for the same number of SNPs, but there can be advantages to this redundancy: loss of a particular SNP to QC filters may not be as costly; and signals of association are likely to include more SNPs, thus making them easier to distinguish from genotyping artefacts.
