paturley

Do you have the log file for the 4-trait maxFDR run and one of the 2-trait maxFDR runs? On Wed, Dec 1, 2021 at 9:43 AM pjordab ***@***.***> wrote: >...

It looks like several lines may be missing from your 2-trait log file. I don't see any lines about the maxFDR calculation. On Fri, Dec 17, 2021 at 2:53 PM...

Alright. What I think is likely happening is that with more traits, there are more ways that the assumptions of MTAG can be violated. For example, with only 2 traits,...

Hi @nay421, You don't need to standardize the phenotype, but whether or not you do so, MTAG results will correspond to a phenotype that had been standardized (but the genotype...

Honestly, I'm not sure why a person would want to use the std-betas option. MTAG by default uses Z-statistics to do its analysis, which means the results are in standardized...

Hello Zongchan, In the paper, we give a rule-of-thumb recommendation of rg>0.7, but it will depend on your application and sample size. I recommend you run the maxFDR calculation to...

Hello, MTAG has a QC check looking at the median betahat estimate. Since the sign of a GWAS coefficient is more or less randomly assigned, the median effect size should...

It really is unusual for the median summary statistic to be so large. Have you checked your data to make sure that the distribution of your betas looks right? Is...

When you calculate the median of your z-scores, do you get a number near 0.11? On Thu, Jun 25, 2020 at 6:18 PM joeyinjie wrote: > I have exactly the...

Hmm. So it's pretty unlikely that the median z-statistic over a million SNPs would be as large as 0.1 unless (1) there is something pretty unique about the phenotype (like...