I want to conduct an exploratory factor analysis on a small questionnaire that I have. The questionnaire consists of 20 items (N=100) that are scored on a 1-5 Likert scale (strongly agree - strongly disagree). I want to perform an EFA with polychoric correlations (principal axis factoring as the variables are non normal), parallel analysis to obtain the amount of factors, and oblique rotation (as the variables are almost always correlated).
However, besides the 1-5 Likert answering options there was also an option "(0) does not apply". I have read numerous books/articles on the subject, but can't seem to find an answer on what I should do with the 0's? Should I use listwise deletion (this will result in a smaller sample size) or should I set the 0 to missing? I want to use FACTOR for the analysis, they have an option for missing data using hot deck imputation. However, I don't know if changing the 0's to missing is ill-advised.
I hope someone has an answer for me. Anyway, thank you in advance for your valuable time.
Fabrigar, L. R., & Wegener, D. T. (2011). Exploratory Factor Analysis (1 edition). Oxford ; New York: Oxford University Press.
Gaskin, C. J., & Happell, B. (2014). On exploratory factor analysis: A review of recent evidence, an assessment of current practice, and recommendations for future use. International Journal of Nursing Studies, 51(3), 511–521. https://doi.org/10.1016/j.ijnurstu.2013.10.005
Norris, M., & Lecavalier, L. (2010). Evaluating the Use of Exploratory Factor Analysis in Developmental Disability Psychological Research. Journal of Autism and Developmental Disorders, 40(1), 8–20. https://doi.org/10.1007/s10803-009-0816-2