Hi everyone I have created 12 pairs of DGE for my 3x2 design matrix with deseq2 and 10/12 shrinking by ashr works fine however,for 2 of the pairs, this message appears

Optimization failed to converge. Results may be unreliable. Try increasing maxiter and rerunning.

I saw error in a thread here https://github.com/stephens999/ashr/issues/76 Does installing mixsqp to resolve this issue? Am I missing anything else?

ashr is a CRAN package and is not part of Bioconductor. I suggest that you post an issue on the GitHub page, and/or add a comment to the pre-existing issue to which you have linked in your question here.