Bioinformatics: tSNE Perplexity parameter

Question

[tom5]

Hi, I hope you're well. I am going through the 'Orchestrating Single-Cell Analysis with Bioconductor' tutorial found here tutorial and am unsure what the perplexity parameter is. Specifically, the guide mentions that this param should be set to less than K, without further guidance. What is K and how do I choose my perplexity?

[Kevin Blighe]

I have alerted the authors of the OSCA book.

[Kevin Blighe]

Could you post this on the Bioconductor support site where the authors will pick it up? - thanks. https://support.bioconductor.org/