puma: a Bioconductor package for propagating uncertainty in microarray analysis |
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| Authors: | Richard D Pearson Xuejun Liu Guido Sanguinetti Marta Milo Neil D Lawrence and Magnus Rattray |
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| Institution: | (1) School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK;(2) Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK;(3) College of Information Science and Technology, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, 210016, PR China;(4) Department of Computer Science, University of Sheffield, Regent Court 211 Portobello Street, Sheffield, S1 4DP, UK;(5) Department of Chemical and Process Engineering, ChELSI Institute, , University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK;(6) NIHR Cardiovascular Biomedical Research Unit, Sheffield Teaching Hospitals NHS Trust, Beech Hill Road, Sheffield, S10 2RX, UK |
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| Abstract: | Background Most analyses of microarray data are based on point estimates of expression levels and ignore the uncertainty of such estimates.
By determining uncertainties from Affymetrix GeneChip data and propagating these uncertainties to downstream analyses it has
been shown that we can improve results of differential expression detection, principal component analysis and clustering.
Previously, implementations of these uncertainty propagation methods have only been available as separate packages, written
in different languages. Previous implementations have also suffered from being very costly to compute, and in the case of
differential expression detection, have been limited in the experimental designs to which they can be applied. |
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