paturley

Hello, Thanks for your detailed question: 1) MTAG should be just fine if your samples are overlapping. Even if they are perfectly overlapping. The interpretation of the results are the...

Hi Anne, 1. The mean chi2 is a function of the sample size and the heritability of your phenotype. So I don't know that you can increase the mean chi2...

1. I think MTAG should be fine if you use mixed models though to be honest I haven't tested it. The key assumption of LDSC that makes h2 estimates wrong...

Hello, Can you attach the complete log file? Hard to debug without it. Patrick On Tue, Apr 5, 2022 at 7:18 AM Mahantesh Biradar ***@***.***> wrote: > I'm trying to...

Hi, It's hard to diagnose this problem without the full log file. Are you able to share it? Patrick On Tue, Apr 5, 2022 at 10:59 AM Mahantesh Biradar ***@***.***>...

Hi Mahantesh, I received your email, but you've only sent a few lines of the log file from your run, so It is difficult to diagnose what is wrong. Are...

It appears to be breaking down on the step when the associations are divided by maf*(1-maf), so my best guess is that some of the SNPs have an allele frequency...

Hello, I presume that it is just taking too long to converge with so many phenotypes. As it says in the MTAG paper "Since p has 2^T elements, [maxFDR] may...

Hello, Aihua! It should be. One of the first steps of the MTAG program is to filter the SNPs down to the intersection of all the GWAS files. Best, Patrick...

In the MTAG paper, the MTAG and GWAS z-stats were only similar when the MTAG was based on a subsets of the UKB and the GWAS was based on the...