Brief. Bioinformatics - Generic framework for high-dimensional fixed-effects ANOVA.

Tópicos

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Resumo

In functional genomics it is more rule than exception that experimental designs are used to generate the data. The samples of the resulting data sets are thus organized according to this design and for each sample many biochemical compounds are measured, e.g. typically thousands of gene-expressions or hundreds of metabolites. This results in high-dimensional data sets with an underlying experimental design. Several methods have recently become available for analyzing such data while utilizing the underlying design. We review these methods by putting them in a unifying and general framework to facilitate understanding the (dis-)similarities between the methods. The biological question dictates which method to use and the framework allows for building new methods to accommodate a range of such biological questions. The framework is built on well known fixed-effect ANOVA models and subsequent dimension reduction. We present the framework both in matrix algebra as well as in more insightful geometrical terms. We show the workings of the different special cases of our framework with a real-life metabolomics example from nutritional research and a gene-expression example from the field of virology.

Resumo Limpo

function genom rule except experiment design use generat data sampl result data set thus organ accord design sampl mani biochem compound measur eg typic thousand geneexpress hundr metabolit result highdimension data set under experiment design sever method recent becom avail analyz data util under design review method put unifi general framework facilit understand dissimilar method biolog question dictat method use framework allow build new method accommod rang biolog question framework built well known fixedeffect anova model subsequ dimens reduct present framework matrix algebra well insight geometr term show work differ special case framework reallif metabolom exampl nutrit research geneexpress exampl field virolog

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