I followed up PLHIV for 6 months collecting monthly data from them. Three patients died before the 6 months follow-up period. How do I handle the 3 deaths in analysis? What do I do to the data collected from them before death?
What are the primary aims of the analysis? What's the endpoint? Without knowing what kind of analysis and hypotheses you're testing it's hard to answer.
Just guessing, but maybe a mixed effects model approach would be the best way to handle the missing data. Although I assume the data is not missing at random. Multiple imputation to replace the missing data could maybe be another option, but we would need more information to better understand the situation.