Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis |
| |
Authors: | Kutalik Zoltan Inwald Jacqueline Gordon Steve V Hewinson R Glyn Butcher Philip Hinds Jason Cho Kwang-Hyun Wolkenhauer Olaf |
| |
Institution: | Control Systems Centre, Department of Electrical Engineering and Electronics, P.O. Box 88, UMIST, Manchester M60 1QD, UK. |
| |
Abstract: | MOTIVATION: When analyzing microarray data, non-biological variation introduces uncertainty in the analysis and interpretation. In this paper we focus on the validation of significant differences in gene expression levels, or normalized channel intensity levels with respect to different experimental conditions and with replicated measurements. A myriad of methods have been proposed to study differences in gene expression levels and to assign significance values as a measure of confidence. In this paper we compare several methods, including SAM, regularized t-test, mixture modeling, Wilk's lambda score and variance stabilization. From this comparison we developed a weighted resampling approach and applied it to gene deletions in Mycobacterium bovis. RESULTS: We discuss the assumptions, model structure, computational complexity and applicability to microarray data. The results of our study justified the theoretical basis of the weighted resampling approach, which clearly outperforms the others. |
| |
Keywords: | |
本文献已被 PubMed Oxford 等数据库收录! |
|