I am using DEXseq for larger samples 70 vs 80. I always got a error. I found a solution at: Efficiently running DEXSeq for Large Cohorts But I think it is out of date.
My code and error are follow.
dxr <- DEXSeq(dxd2, BPPARAM=MulticoreParam(workers=50))
Error in value[[3L]](cond) : setting worker timeout:
error reading from connection
In addition: Warning message:
In rm(list = cuid, envir = env) : object '1' not found
I'd be surprised if having many workers is helpful. Have you investigated how performance changes with SerialParam() an then MulticoreParam() with just a few (2, 5, 10) workers?