There is no one to ask about the analysis process, please advise to me.
I'd like to do perform association test between case and control group.
First of all, I made 'phenotype.txt' coded as 0, 1.
As I'm not sure, I did 3 kind of association works for all samples, case samples, and control samples.
1. ./plink --noweb --bfile <all data> --assoc --pheno <phenotype.txt> --out <new file> 2. /plink --noweb --bfile <case data> --assoc --pheno <phenotype.txt> --out <new file> 3. /plink --noweb --bfile <control data> --assoc --pheno <phenotype.txt> --out <new file>
(maybe of course,) the top SNPs on each Manhattan plot were different, likewise on p-value.
Then, can I choose the specific SNPs from the case data for the phenotype, and understand the SNPs might affect the phenotype?
Or, since the process has a problem, do I have to do other methods?
Making a new PED file coded 'affection' column as one of 'phenotype.txt'?
Please help and hope to advice. Thank you.