It is well known that dimensionality reduction based on multivariate analysis methods and their kernelized extensions can be formulated as generalized eigenvalue problems of scatter matrices, Gram matrices or their augmented matrices. This paper provides a generic and theoretical framework of multivariate analysis introducing a new expression for scatter matrices and Gram matrices, called Generalized Pairwise Expression (GPE). This expression is quite compact but highly powerful. The framework includes not only (1) the traditional multivariate analysis methods but also (2) several regularization techniques, (3) localization techniques, (4) clustering methods based on generalized eigenvalue problems, and (5) their semi-supervised extensions. This paper also presents a methodology for designing a desired multivariate analysis method from the proposed framework. The methodology is quite simple: adopting the above mentioned special cases as templates, and generating a new method by combining these templates appropriately. Through this methodology, we can freely design various tailor-made methods for specific purposes or domains.