Right now i have done QC' ing using PLINK, for my Geno-typed data. I was looking for conducting Gender stratification, I have the following concerns/doubts which i am not able to solve. It would be great if you guys help me out.
1 - Gender stratification, if p values is consistently low, even on statistical correction, what can be done ? 2- How to Overlay MY SNP data with other major studies (Case control studies), and is their any databases where the genotype data is stored? 3- I have the Geno typed data with me, what all the other analysis can be done on it ?
I know this might be very silly questions, for a novice like me ......... its worth millions ! i am really feeling the heat of it. so, sorry for annoyance (in case)
Thanks a lot for your help !