paturley

Hello, In general, the main things that affect the mean chi2 statistic of a GWAS is the heritability of the phenotype and the sample size available. So other than considering...

I can't think of why a sex imbalance would create problems for MTAG as long as the assumptions of MTAG are met. Generally, MTAG inherits the biases of the input...

Yeah, this is confusing to me. The diagonal elements of Omega shouldn't be negative. This sometimes can occur when the sample size is small (which doesn't seem to be the...

Hmm. The problem seems to be in the Omega calculation. How comfortable are you with Python? In your local copy, if you can temporarily modify the gmm_omega function on line...

This would be easier to diagnose if you shared the full log file. Best, Patrick On Fri, Nov 3, 2023 at 1:58 PM samreenzafer ***@***.***> wrote: > @nadineparker Any luck...

Have you plotted a histogram of your z-scores? This error is meant to identify irregularities in the distribution of the test statistics. On Fri, Dec 16, 2022 at 5:08 PM...

Curious. Yep. And that histogram looks a little left-skewed, but not so much that I would be worried. I see you only have ~100k SNPs in your sumstats. That seems...

Very funny. If you are confident that the sumstats are right but just oriented so the z-stat is negative, you could just reorient the sumstats such that they correspond to...

Hmm. Assuming that there is nothing funny with your summary statistics and that MTAG is reading the right columns, setting the median z cutoff to some high value like that...

Yes, that's right. The output of MTAG are marginal effects with the same interpretation as what you'd get from a GWAS. On Wed, Sep 20, 2023 at 3:51 AM Angli...