Lassana1

Thanks! Yes, I tried running all the other traits. I get a warning message "Removed 2783019 SNPs with missing values". What is the meaning of this error?

Hi, I am attaching my log here. I reran a new analysis with traits where chi2 > 1, and also changed the freq values(my old calculations were wrong). 1) I...

Looking at the results from this analysis, some traits have alot of missing mtag_pvalues. These are the no of missing p values: trait1- 147347 trait2- 8851014 trait3- 8883262 trait4- 79833...

Hi Patrick, you are right! Actually trait 5 was highly correlated with all the other traits. So I dropped traits2 and 5, and ran MTAG on 3 traits of interest....

Hi, I also realized a warning in the log file "sigma matrix used is still not positive definite". Does this invalidate the results output from the mtag analysis?

Hi, so I repeated the above analysis, but included variants. I used the methods proposed in issue #59 to "change no_alleles=False to no_alleles=True in line [154] and [156] of mtag.py"....

Hi Patrick, thanks so much! Sorry, I should have mentioned before that my samples have a perfect overlap, and they are summary stats from the HCHS SOL cohort. I will...

Hi Patrick, Below is the correlation matrix for my phenotypes, (calculated using spearman method on the beta estimates for each trait) for which I inputted into MTAG analysis using --residcov_path...

Hi Patrick, thank you for the clarification and all your help. I do have the raw data. A sample set of 7605 was used to carry out all GWAS analysis....

Hi, so I calculated a phenotype matrix, assuming the sample overlap is perfect, which is pretty close to the sigma hat calculated in mtag. phenotype matrix- [[ 1. 0.363 0.471]...