I have SNP data of a Illumina HumanOmni5-4 BeadChip (4.2 million SNPs) for 28 samples with a quantitative trait. I have no experience doing GWAS studies and I need some advice. So far, I performed the quality control steps suggested by the GWASTools Vignette.
Which testing procedure is best for this kind of data? It seems, such a small number of samples leads to no significant p-values. Any way to improve this? Should I use the quantitative trait directly with linear regression based testing or does it make any sense to group the samples and do a case-control study?
Any suggestion would be of great help to me!