Stability and aggregation of ranked gene lists

Ranked gene lists are highly instable in the sense that similar measures of differential gene expression may yield very different rankings, and that a small change of the data set usually affects the obtained gene list considerably. Stability issues have long been under-considered in the literature,...

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Bibliographic Details
Published in:Briefings in bioinformatics 2009-09, Vol.10 (5), p.556-568
Main Authors: Boulesteix, Anne-Laure, Slawski, Martin
Format: Article
Language:English
Subjects:
Algorithms
Bioinformatics
Biological and medical sciences
Databases, Genetic
Fundamental and applied biological sciences. Psychology
Gene expression
Gene Expression Profiling - methods
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Models, Genetic
Models, Statistical
Molecular biology
Oligonucleotide Array Sequence Analysis - methods
Software
Statistical analysis
Statistical methods
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Summary:Ranked gene lists are highly instable in the sense that similar measures of differential gene expression may yield very different rankings, and that a small change of the data set usually affects the obtained gene list considerably. Stability issues have long been under-considered in the literature, but they have grown to a hot topic in the last few years, perhaps as a consequence of the increasing skepticism on the reproducibility and clinical applicability of molecular research findings. In this article, we review existing approaches for the assessment of stability of ranked gene lists and the related problem of aggregation, give some practical recommendations, and warn against potential misuse of these methods. This overview is illustrated through an application to a recent leukemia data set using the freely available Bioconductor package GeneSelector.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbp034