I have just recently noticed a potentially fatal flaw in my analysis regarding which dataset to use as base and target, and would like to confirm with a professional.
This is my current situation:
My dataset is called MATCH (which is what I want to calculate PRSs for), and for the analysis I am using the GSCAN (GWAS and Sequencing Consortium of Alcohol and Nicotine use) study. In my case, I have used the GSCAN summary statistics as the base and the MATCH dataset as the target. I have also used the phenotype files from the MATCH study to do the analysis. I was wondering if this is considered incorrect for PRSice usage regarding the use of base and target datasets. I really appreciate your time and insight, many thanks in advance!
Hi,
Apologies for posting during the weekend.
I have just recently noticed a potentially fatal flaw in my analysis regarding which dataset to use as base and target, and would like to confirm with a professional.
This is my current situation:
My dataset is called MATCH (which is what I want to calculate PRSs for), and for the analysis I am using the GSCAN (GWAS and Sequencing Consortium of Alcohol and Nicotine use) study. In my case, I have used the GSCAN summary statistics as the base and the MATCH dataset as the target. I have also used the phenotype files from the MATCH study to do the analysis. I was wondering if this is considered incorrect for PRSice usage regarding the use of base and target datasets. I really appreciate your time and insight, many thanks in advance!
Best, Paulo