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Novel Methods for Multivariate Ordinal Data applied to Genetic Diplotypes, Genomic Pathways, Risk Profiles, and Pattern Similarity

Wittkowski, Knut M. (2003): Novel Methods for Multivariate Ordinal Data applied to Genetic Diplotypes, Genomic Pathways, Risk Profiles, and Pattern Similarity. Published in: Computational Science and Statistics , Vol. 35, (2003): pp. 626-646.

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Abstract

Introduction: Conventional statistical methods for multivariate data (e.g., discriminant/regression) are based on the (generalized) linear model, i.e., the data are interpreted as points in a Euclidian space of independent dimensions. The dimensionality of the data is then reduced by assuming the components to be related by a specific function of known type (linear, exponential, etc.), which allows the distance of each point from a hyperspace to be determined. While mathematically elegant, these approaches may have shortcomings when applied to real world applications where the relative importance, the functional relationship, and the correlation among the variables tend to be unknown. Still, in many applications, each variable can be assumed to have at least an “orientation”, i.e., it can reasonably assumed that, if all other conditions are held constant, an increase in this variable is either “good” or “bad”. The direction of this orientation can be known or unknown. In genetics, for instance, having more “abnormal” alleles may increase the risk (or magnitude) of a disease phenotype. In genomics, the expression of several related genes may indicate disease activity. When screening for security risks, more indicators for atypical behavior may constitute raise more concern, in face or voice recognition, more indicators being similar may increase the likelihood of a person being identified.

Methods: In 1998, we developed a nonparametric method for analyzing multivariate ordinal data to assess the overall risk of HIV infection based on different types of behavior or the overall protective effect of barrier methods against HIV infection. By using u-statistics, rather than the marginal likelihood, we were able to increase the computational efficiency of this approach by several orders of magnitude.

Results: We applied this approach to assessing immunogenicity of a vaccination strategy in cancer patients. While discussing the pitfalls of the conventional methods for linking quantitative traits to haplotypes, we realized that this approach could be easily modified into to a statistically valid alternative to a previously proposed approaches. We have now begun to use the same methodology to correlate activity of anti-inflammatory drugs along genomic pathways with disease severity of psoriasis based on several clinical and histological characteristics.

Conclusion: Multivariate ordinal data are frequently observed to assess semiquantitative characteristics, such as risk profiles (genetic, genomic, or security) or similarity of pattern (faces, voices, behaviors). The conventional methods require empirical validation, because the functions and weights chosen cannot be justified on theoretical grounds. The proposed statistical method for analyzing profiles of ordinal variables, is intrinsically valid. Since no additional assumptions need to be made, the often time-consuming empirical validation can be skipped.

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