paturley

Wonderful. Glad it worked. On Wed, Aug 22, 2018 at 1:04 PM cks2903 wrote: > Thank you, that solved my problem! > > — > You are receiving this because...

The mean chi2 statistic is the mean value of the chi2 statistic (or the square of the z-statistic) across the SNPs in your data. It's equal to one (in expectation)...

Hello! I think the likely culprit here is that your mean chi2 statistics are too small for MTAG to work well. MTAG estimates the variance of the effect sizes using...

I would be suspicious of p-values for all of the traits in an analysis where any of the traits has a p-value of less than one. It may be fine,...

The software may run if you use the force option, but you should be careful. This error gets thrown when one or more of the GWAS results are low powered,...

MTAG uses a reference genome to run LD score regression. If you are not using a human sample, you may need to calculate the LD scores yourself for MTAG to...

It sounds as if I was mistaken and MTAG can't take user-generated LD scores. (Correct me if I'm wrong, Hui.) If you want to put in the work, I think...

It's the Sigma matrix that requires LD score regression. I don't recall the exact format the is required for the file, but Hui should be able to help there. Will...

In that case, you may need to dig into the code and comment out the lines where the SNPs are compared to the reference SNP list. I imagine the code...

The summary table in your log file seems to be abbreviated and it omits the GWAS n and the original chi2 statistics that used in the GWAS-equiv N calculation, so...