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jsh58 / DMRfinder

Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data
MIT License
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Multiple Errors with dispersion.shrinkage.BSseq #12

Closed npatel22526 closed 4 years ago

npatel22526 commented 4 years ago

Hello, I was trying to run the DMRfinder.R script the way it's described in Readme , however, getting below error. It seems they both coming from a DSS utility

Error 1 : I try fixing this by adding variable ncores =1

Comparing group "Control" to group "Disease" Estimating dispersion for each CpG site, this will take a while ... Error in est.dispersion.BSseq(cbind(x1, x2), cbind(n1, n2), cbind(estprob1, : object 'ncores' not found Calls: DMLtest ... est.dispersion.BSseq -> dispersion.shrinkage.BSseq -> bpworkers Execution halted

Error2 : Comparing group "Control" to group "Disease" Estimating dispersion for each CpG site, this will take a while ... Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘bpworkers’ for signature ‘"numeric"’ Calls: DMLtest ... dispersion.shrinkage.BSseq -> bpworkers -> Execution halted

Thanks, Nick

jsh58 commented 4 years ago

Nick,

Thanks for the question. This may be an issue with DSS. Are you using version 2.14.0? That is the version I tested on, and I did not encounter such an error.

John Gaspar

npatel22526 commented 4 years ago

Hello John, Thanks, Yes, replacing current DSS (2.34.0) with DSS 2.14.0 solved the problem.

Best, Nick