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Bioinformatics Advance Access originally published online on September 6, 2005
Bioinformatics 2005 21(20):3840-3845; doi:10.1093/bioinformatics/bti641
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Shifting and scaling patterns from gene expression data

Jesús S. Aguilar-Ruiz

BIGS BioInformatics Group Seville, University of Seville, Pablo de Olavide University Spain

Motivation: During the last years, the discovering of biclusters in data is becoming more and more popular. Biclustering aims at extracting a set of clusters, each of which might use a different subset of attributes. Therefore, it is clear that the usefulness of biclustering techniques is beyond the traditional clustering techniques, especially when datasets present high or very high dimensionality. Also, biclustering considers overlapping, which is an interesting aspect, algorithmically and from the point of view of the result interpretation. Since the Cheng and Church's works, the mean squared residue has turned into one of the most popular measures to search for biclusters, which ideally should discover shifting and scaling patterns.

Results: In this work, we identify both types of patterns (shifting and scaling) and demonstrate that the mean squared residue is very useful to search for shifting patterns, but it is not appropriate to find scaling patterns because even when we find a perfect scaling pattern the mean squared residue is not zero. In addition, we provide an interesting result: the mean squared residue is highly dependent on the variance of the scaling factor, which makes possible that any algorithm based on this measure might not find these patterns in data when the variance of gene values is high. The main contribution of this paper is to prove that the mean squared residue is not precise enough from the mathematical point of view in order to discover shifting and scaling patterns at the same time.

Contact: aguilar{at}lsi.us.es

Received on May 24, 2005; revised on August 7, 2005; accepted on August 22, 2005

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[Abstract] [Full Text] [PDF]


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