Question
Question Posted 03/13/24:
I downloaded the ADNI genetic data to do GWAS research, I get the data in plink format where I was able to get the three files of .bed, .bim and .fam, however as the fam file has the individuals info like the id the sex and other info, I know that the last attribute is the trait or phenotype which should be either like 1 (cases) and 2 (controls), however the values that i found is -9 which means it's missing so can I please get some advise if i am downloading the correct data or what I should do
I downloaded the ADNI genetic data to do GWAS research, I get the data in plink format where I was able to get the three files of .bed, .bim and .fam, however as the fam file has the individuals info like the id the sex and other info, I know that the last attribute is the trait or phenotype which should be either like 1 (cases) and 2 (controls), however the values that i found is -9 which means it's missing so can I please get some advise if i am downloading the correct data or what I should do
Response posted 03/13/24 by Kwangsik Nho:
In the plink files, you need to update the diagnosis information based on your research strategy. Currently the diagnosis information was missed in the plink files.
