I have merged two datasets from different platforms after imputation (Dataset1 includes 20 cases and 2000 controls, and about 450000 SNPs per chromosome. Dataset2 includes 5 cases, and about 150000 SNPs per chromosome). I adjusted the MAP files in both datasets as there were multiple SNP IDs with the same positions, and, in addition, I excluded the 200 SNPs from both datasets as which were possibly genotyping errors in dataset2. Subsequently I confirmed that all cases and controls are all in the same population. Then common SNPs in both datasets are only 150000 SNPs per chromosome, thus, I extracted those SNPs in both datasets and merged two datasets. Then I conducted association analysis after QC in plink.
The qq plot of p-values are inflated and genomic inflation ext. lambda (based on median chisq) was 1.2. Would anybody have ideas about what is wrong?
Thank you in advance!