General Effect Modelling (GEM) is an umbrella over different methods that utilise effects in the analyses of data with multiple design variables and multivariate responses. To demonstrate the methodology, we here use GEM in gene expression data where we use GEM to combine data from different cohorts and apply multivariate analysis of the effects of the targeted disease across the cohorts. Omics data are by nature multivariate, yet univariate analysis is the dominating approach used for such data. A major challenge in omics data is that the number of features such as genes, proteins and metabolites are often very large, whereas the number of samples is limited. Furthermore, omics research aims to obtain results that are generically valid across different backgrounds. The present publication applies GEM to address these aspects. First, we emphasise the benefit of multivariate analysis for multivariate data. Then we illustrate the use of GEM to combine data from two different cohorts for multivariate analysis across the cohorts, and we highlight that multivariate analysis can detect information that is lost by univariate validation.

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