Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.

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

SUBMITTER: Tseng GC 

PROVIDER: S-EPMC55725 | biostudies-literature | 2001 Jun

REPOSITORIES: biostudies-literature