Hello,
I noticed that when using very high coverage in the sync file (in my case 2000), I get an error related to the expmat() function saying that the matrix is ill-conditioned. The problem is solved by downscaling the coverage (in my case I scaled it down to 100 coverage).
The only issue here is that the estimation of Ne using poolseq seems to change when using the two coverages (in my case it almost doubles as I scale down the coverage). I tried running Bait-ER specifying either Nes and the results seem consistent with each other, so Ne had very little effect on the results.
I realize that a coverage of 2000 is not very realistic, but it still took me a while to figure out why I got the error, so I think it might be useful to know.
Best
Michele
Hello,
I noticed that when using very high coverage in the sync file (in my case 2000), I get an error related to the expmat() function saying that the matrix is ill-conditioned. The problem is solved by downscaling the coverage (in my case I scaled it down to 100 coverage).
The only issue here is that the estimation of Ne using poolseq seems to change when using the two coverages (in my case it almost doubles as I scale down the coverage). I tried running Bait-ER specifying either Nes and the results seem consistent with each other, so Ne had very little effect on the results.
I realize that a coverage of 2000 is not very realistic, but it still took me a while to figure out why I got the error, so I think it might be useful to know.
Best
Michele