The RunPCA() in Seurat 3.0 function has seed.use=42 by default. How does one choose a seed number? Is this chosen simply because it is the Answer to the Ultimate Question of Life, the Universe, and Everything? Or maybe Lewis Carroll's curious obsession with the number?
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Given that it is virtually impossible for a human to predict what random numbers will be generated given a certain seed, and what effects they will have for a given application, the choice of the seed can be considered arbitrary.
What matters is that fixing the seed should fix the behaviour of the application. What seed has been chosen does not really matter, as long as it is documented.
The choice of 42 could therefore well come from one of the reasons you propose. Only the authors of the programs could confirm.
42is a popular choice for the reasons you note, residentmar.io/2016/07/08/randomly-popular.html and blog.semicolonsoftware.de/the-most-popular-random-seeds $\endgroup$