Identifying differentially expressed genes in dye-swapped microarray experiments of small sample size

• Published in: Computational statistics & data analysis 2007-02, Vol.51 (5), p.2602-2620
• Main Authors: Lian, I.B., Chang, C.J., Liang, Y.J., Yang, M.J., Fann, C.S.J.
• Format: Article
• Language: English
• Subjects: ANOVA; Dye-swapped design; Exact sciences and technology; General topics; Mathematics; Multivariate analysis; Numerical analysis; Numerical analysis. Scientific computation; Numerical methods in probability and statistics; Probability and statistics; Robust regression; Sampling theory, sample surveys; Sciences and techniques of general use; Statistics; Two color microarray
• ISSN: 0167-9473; 1872-7352
• DOI: 10.1016/j.csda.2006.01.003

When using microarray analysis to determine gene dependence, one of the goals is to identify differentially expressed genes. However, the inherent variations make analysis challenging. We propose a statistical method (SRA, swapped and regression analysis) especially for dye-swapped design and small sample size. Under general assumptions about the structure of the channels, scanner, and target effects from the experiment, we prove that SRA removes bias caused by these effects. We compare our method with ANOVA, using both simulated and real data. The results show that SRA has consistent sensitivity for the identification of differentially expressed genes in dye-swapped microarrays, particularly when the sample size is small. The program for the proposed method is available at http://www.ibms.sinica.edu.tw/ ∼ csjfann/firstflow/program.htm .