Closed cwoehle closed 2 years ago
Hi Christian, thanks for bringing this up, I never noticed because I always run them with multithreading, but you're probably not the only user that will face this. Yes I'd use your solution, and I now added this in the vignette (in the FAQ on reproducibility). Best, plger
Hi Pierre-Luc,
Yes I'd use your solution, and I now added this in the vignette (in the FAQ on reproducibility).
Not sure you what you were referring to here, but if this is this section of the vignette, I still find it confusing...
Could you maybe mention that this way of setting the seed should always be used when the samples
argument is used, even when the default BPPARAM=SerialParam()
is used?
you're right, wasn't clear, hope it is now.
Hello,
I was trying to run scDblFinder with the
samples
parameter,set.seed()
, but withoutBPPARAM
and noticed that reproducibility was not given (Finding the same number of doublets). Either removing thesamples
parameter or addingBPPARAM=MulticoreParam(1, RNGseed=seed)
produced reproducible results. However, I was searching for a way for serial execution suitable for running in RStudio (I keep having problems with BiocParallel) and needed to consider individual samples. So, after some testing I ended up usingBPPARAM=SerialParam(RNGseed = seed)
, which seems to lead to the behaviour I was looking for. I did not find any comment onSerialParam()
in the documentation. Would this also be your suggested solution in my case or could there be a better alternative?I´m grateful for any clarification.
Best wishes, Christian