Issues in cDNA Microarray Analysis: Quality Filtering, Channel Normalization, Models of Variations and Assessment of Gene Effects

Nucleic Acids Res. 2001 Jun 15;29(12):2549-57. doi: 10.1093/nar/29.12.2549.

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.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Acetic Acid / metabolism
  • Calibration
  • DNA, Complementary / genetics
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Gene Expression Profiling / methods*
  • Gene Expression Profiling / standards
  • Gene Expression Regulation, Bacterial*
  • Genes, Bacterial / genetics*
  • Glucose / metabolism
  • Mathematics
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Array Sequence Analysis / standards
  • Quality Control
  • RNA, Bacterial / analysis
  • RNA, Bacterial / genetics
  • RNA, Bacterial / isolation & purification
  • Reference Standards
  • Research Design
  • Terminology as Topic

Substances

  • DNA, Complementary
  • RNA, Bacterial
  • Glucose
  • Acetic Acid