whys lambda is so large

[koujiaodahan]

I try to run fitted_rss1 <- susie_rss(bhat = sumread$beta_alt, shat = sumread$V10, n = N, R = ldmatrix, L = 10,
estimate_residual_variance = FALSE,verbose=TRUE)
based on my gwas summary statistics and the LD matrix of same samples.
After that,I run kriging_rss for diagnose. but the lambda is always above 0.4
and the plot is that. why?

[koujiaodahan]

Besides that , running the susie_rss function at a locus(chr6), it breaks with "Error in susie_suff_stat(XtX = XtX, Xty = Xty, n = n, yty = (n - 1) * :
The estimated prior variance is unreasonably large.
This is usually caused by mismatch between the summary statistics and the LD matrix.
Please check the input.
Calls: susie_rss -> susie_suff_stat
Execution halted"

[stephens999]

The results suggest something wrong with the way you are computing your ld matrix or z scores