Deterministic parallel analysis

Factor analysis is widely used in many application areas. The first step, choosing the number of factors, remains a serious challenge. One of the most popular methods is parallel analysis (PA), which compares the observed factor strengths to simulated ones under a noise-only model. This paper presents a deterministic version of PA (DPA), which is faster and more reproducible than PA. We show that DPA selects large factors and does not select small factors just like Dobriban (2017) shows for PA. Both PA and DPA are prone to a shadowing phenomenon in which a strong factor makes it hard to detect smaller but more interesting factors. We develop a deflated version of DPA (DDPA) that counters shadowing. By raising the decision threshold in DDPA, a new method (DDPA+) also improves estimation accuracy. We illustrate our methods on data from the Human Genome Diversity Project (HGDP). There PA and DPA select seemingly too many factors, while DDPA+ selects only a few. A Matlab implementation is available.