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

Iebin Lian, C. J. Chang, Y. J. Liang, M. J. Yang, C. S J Fann

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)2602-2620
Number of pages19
JournalComputational Statistics and Data Analysis
Volume51
Issue number5
DOIs
Publication statusPublished - 2007 Feb 1

Fingerprint

Small Sample Size
Microarrays
Dyes
Regression Analysis
Microarray
Regression analysis
Genes
Gene
Experiment
Microarray Analysis
Experiments
Analysis of variance (ANOVA)
Scanner
Statistical method
Statistical methods
Sample Size
Target
Small sample
Sample size

All Science Journal Classification (ASJC) codes

  • Computational Theory and Mathematics
  • Statistics, Probability and Uncertainty
  • Electrical and Electronic Engineering
  • Computational Mathematics
  • Numerical Analysis
  • Statistics and Probability

Cite this

Lian, Iebin ; Chang, C. J. ; Liang, Y. J. ; Yang, M. J. ; Fann, C. S J. / Identifying differentially expressed genes in dye-swapped microarray experiments of small sample size. In: Computational Statistics and Data Analysis. 2007 ; Vol. 51, No. 5. pp. 2602-2620.
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Identifying differentially expressed genes in dye-swapped microarray experiments of small sample size. / Lian, Iebin; Chang, C. J.; Liang, Y. J.; Yang, M. J.; Fann, C. S J.

In: Computational Statistics and Data Analysis, Vol. 51, No. 5, 01.02.2007, p. 2602-2620.

Research output: Contribution to journalArticle

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