I'm just getting into working with SNP arrays after a while of working with gene expression data. We've got a small dataset (12 samples) of SNP arrays (Illumina Human Omni 5) which represent disease case and control. We don't have family data. Obviously 12 samples is much too small for a GWAS. I ran PennCNV already, but there has to be more I can look at with this- any suggestions? The data I have available is derived from Illumina "Final Report" files- Allele1-Top, Allele2-Top, and the B-allele frequency and Log R ratio.