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stephenslab / flashr

R package for Empirical Bayes Factor Analysis.
https://stephenslab.github.io/flashr
BSD 3-Clause "New" or "Revised" License
49 stars 11 forks source link

remove seed parameter? #80

Closed willwerscheid closed 6 years ago

willwerscheid commented 6 years ago

I think we can trust the user to set seeds when necessary. softImpute, for example, doesn't include a seed parameter. Nor does glmnet, etc... the usual practice seems to be to leave it out.

pcarbo commented 6 years ago

@willwerscheid Agreed!

stephens999 commented 6 years ago

i’d much rather keep the seed as it seems a sensible default to set the seed and make things produce the same answer every time…. i would argue this is standard (and best) practice with command line programs. eg I do that in PHASE. From experience i think it is optimistic to trust users to do this (including ourselves!)

On Fri, Aug 24, 2018 at 10:03 AM Peter Carbonetto notifications@github.com wrote:

@willwerscheid https://github.com/willwerscheid Agreed!

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