We are doing GWAS study related to fruits colour by using PLINK 1.9. Color intensity (RED, GREEN & BLUE channel ) of fruit's color is used as phenotype for this study. The genomic inflation is 2.2 after association test (--pheno pheno.txt --linear hide-covar --adjust qq-plot --all-pheno) .We were able to reduce genomic inflation to 1.7 & 1.3 when we used top 20 PCA and top 3 PCA as covar. Please any one can suggest me that how to choose the best PCAs to reduce the genomic inflation? Is any other way to reduce genomic inflation other than PCA ?
Thanks in advance .