title: Parallel classification and feature selection in microarray data using SPRINT.
abstract: The statistical language R is favoured by many biostatisticians for processing microarray data. In recent times, the quantity of data that can be obtained in experiments has risen significantly, making previously fast analyses time consuming or even not possible at all with the existing software infrastructure. High performance computing (HPC) systems offer a solution to these problems but at the expense of increased complexity for the end user. The Simple Parallel R Interface is a library for R that aims to reduce the complexity of using HPC systems by providing biostatisticians with drop-in parallelised replacements of existing R functions. In this paper we describe parallel implementations of two popular techniques: exploratory clustering analyses using the random forest classifier and feature selection through identification of differentially expressed genes using the rank product method.
authors.affiliation: EPCC, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3JZ, UK.
authors.forename: Lawrence
authors.initials: L
authors.lastname: Mitchell
authors.affiliation: EPCC, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3JZ, UK.
authors.forename: Terence M
authors.initials: TM
authors.lastname: Sloan
authors.affiliation: Division of Pathway Medicine, University of Edinburgh, Medical School, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
authors.forename: Muriel
authors.initials: M
authors.lastname: Mewissen
authors.affiliation: Division of Pathway Medicine, University of Edinburgh, Medical School, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Ghazal
authors.affiliation: Division of Pathway Medicine, University of Edinburgh, Medical School, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Forster
authors.affiliation: EPCC, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3JZ, UK.
authors.forename: Michal
authors.initials: M
authors.lastname: Piotrowski
authors.affiliation: EPCC, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3JZ, UK.
authors.forename: Arthur
authors.initials: A
authors.lastname: Trew
keywords: Genomics; HPC; Parallel programming