Issues in cDNA microarray analysis

Quality filtering, channel normalization, models of variations and assessment of gene effects

George C. Tseng, Min-Kyu Oh, Lars Rohlin, James C. Liao, Wing Hung Wong

Research output: Contribution to journalArticle

465 Citations (Scopus)

Abstract

We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the same slide, to filter out outlying spots, poor quality genes and problematical slides. We also perform calibration experiments to show that normalization between fluorescent labels is needed and that the normalization is slide dependent and non-linear. A rank invariant method is suggested to select non-differentially expressed genes and to construct normalization curves in comparative experiments. After normalization the residuals from the calibration data are used to provide prior information on variance components in the analysis of comparative experiments. Based on a hierarchical model that incorporates several levels of variations, a method for assessing the significance of gene effects in comparative experiments is presented. The analysis is demonstrated via two groups of experiments with 125 and 4129 genes, respectively, in Escherichia coli grown in glucose and acetate.

Original languageEnglish
Pages (from-to)2549-2557
Number of pages9
JournalNucleic Acids Research
Volume29
Issue number12
Publication statusPublished - 2001 Jun 15
Externally publishedYes

Fingerprint

Microarray Analysis
Microarrays
Oligonucleotide Array Sequence Analysis
Complementary DNA
Genes
Calibration
Experiments
Acetates
Gene expression
Escherichia coli
Labels
Gene Expression
Glucose
Cells

ASJC Scopus subject areas

  • Genetics

Cite this

Issues in cDNA microarray analysis : Quality filtering, channel normalization, models of variations and assessment of gene effects. / Tseng, George C.; Oh, Min-Kyu; Rohlin, Lars; Liao, James C.; Wong, Wing Hung.

In: Nucleic Acids Research, Vol. 29, No. 12, 15.06.2001, p. 2549-2557.

Research output: Contribution to journalArticle

Tseng, George C. ; Oh, Min-Kyu ; Rohlin, Lars ; Liao, James C. ; Wong, Wing Hung. / Issues in cDNA microarray analysis : Quality filtering, channel normalization, models of variations and assessment of gene effects. In: Nucleic Acids Research. 2001 ; Vol. 29, No. 12. pp. 2549-2557.
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