Dear Mark,
thanks for your answer and for clarifying the data nature, I will keep that in mind.
Regarding your question, I am not sure I get it right. I have two quantitative methods to detect proteins and I want to compare them. If I am not wrong the most appropriate methods (or at least some that I have found on the literature) for comparing such measurements are Bland-Altman plots and Passing-Bablok regression. Is this correct? Any other method you can suggest?
I understand that substituting data introduces bias, but then how can I analyze data with "less than" or "greater than" results? I cannot just ignore it as it provides valuable information (mostly absence of protein but also large amounts of protein on the other hand)
Best,
David