Closed Y-Isaac closed 5 months ago
@Y-Isaac thanks for flagging this. As the warning message says, "The HESS estimator is unconstrained, and the estimate is an order of magnitude greater than the expected max of 1". The HESS estimator is a reasonable estimator in most cases, but like every estimator it has its pitfalls.
I can't fix this, but I updated the code to emit a clearer error message in this case. Sorry I can't provide more help --- hopefully this will help future users
@omerwe HI,
I see the update. I am considering whether it is possible to use the built-in estimator in susie for these erroneous loci, otherwise use HESS? Do you think it is reasonable to have two types of causal effect size estimators coexist in one analysis? Because I feel it's a pity to simply give up on these loci, this solution is a workaround.
@Y-Isaac yes you can definitely do that. Overall the prior variance usually doesn't make a big difference in well-behaved loci, and my opinion is it's better to get results from all loci than giving up on some loci, as long as you remember that some of the loci requires extra scrutiny.
@omerwe You help me a lot! Thanks for your help sincerely, wish you have a nice day!
HI,
I apologize for asking multiple times. When I attempt to use HESS to estimate the variance of causal effect sizes, most of the results appear normal, but some of them encounter the following error message: _"Error in init_setup(0, p, L, scaled_prior_variance, residualvariance, : Scaled prior variance should be no greater than 1 when standardize = TRUE." In fact, the same region can run normally using the built-in estimator in susie. Below is my complete log file, which I hope will be helpful to you: