Nucleic Acids Research, 2001, Vol. 29, No. 12 2549-2557
© 2001 Oxford University Press
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects
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.
* To whom correspondence should be addressed at: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA. Tel: +1 617 432 4912; Fax: +1 617 739 1781; Email: wwong{at}hsph.harvard.edu Correspondence may also be addressed to James C. Liao. Tel: +1 310 825 1656; Fax: +1 310 206 4107; Email: liaoj{at}ucla.edu The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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