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mildpiggy / DEP2

An r package for proteomics data Analysis, developed from DEP.
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`filter_se` parameter `fraction` can be misleading. #21

Closed m-pauper closed 1 day ago

m-pauper commented 2 days ago

Hello, thanks for publishing DEP and DEP2.

I just wanted to give some feedback on filter_se's parameter fraction as I find it a bit misleading. The description says:

"A numeric from 0 to 1, threshold of missing occupancy of each row"

However, setting the threshold at e.g. 0.4, means that a feature can have 60% missing values. I would expect it to mean that 40% missing values is the maximum threshold allowed.

mildpiggy commented 1 day ago

Hi. As you found, my parameter description is not accurate. The fraction should be the valid quantitative fraction (1 - missing ratio). In fact, a larger fraction corresponds to a stricter filtering. Thank you for your observation, and I will modify the description of parameter fraction in future updates.

m-pauper commented 1 day ago

Thanks for the quick reaction!