Targeted projection pursuit for visualizing gene expression data classifications

Authors:
Joe Faith;Robert Mintram;Maia Angelova
Affiliations:
Northumbria University Newcastle, UK;Bournemouth University Bournemouth, UK;Northumbria University Newcastle, UK
Venue:
Bioinformatics
Year:
2006

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Abstract

We present a novel method for finding low-dimensional views of high-dimensional data: Targeted Projection Pursuit. The method proceeds by finding projections of the data that best approximate a target view. Two versions of the method are introduced; one version based on Procrustes analysis and one based on an artificial neural network. These versions are capable of finding orthogonal or non-orthogonal projections, respectively. The method is quantitatively and qualitatively compared with other dimension reduction techniques. It is shown to find 2D views that display the classification of cancers from gene expression data with a visual separation equal to, or better than, existing dimension reduction techniques. Availability: source code, additional diagrams, and original data are available from http://computing.unn.ac.uk/staff/CGJF1/tpp/bioinf.html Contact: joe.faith@unn.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.