I was wondering how I would go about setting the --p-max-depth value when doing alpha rarefaction. I see that the --p-min depth value cannot be less than 0, so that can be ignored, and the max value that you can have for --p-max-depth is your maximum feature count value (in the Moving Pictures tutorial for example, the Maximum frequency in table.qzv is 9820). Is there an optimum value that I can set --p-max-depth to? Why would I set this value higher versus lower?
Great Question and Welcome to the forum!
This is a hard question because there is no optimum value. It is all just what you think is best for your data. I think that Colin gave a really great answer on this post. They explained how they choose their max-depth.
I also would suggest looking at the description of the Parkinson’s mouse tutorial . It really helped me understand.
Hope that helps!
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