Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells

Genome Biol. 2003;4(12):R82. doi: 10.1186/gb-2003-4-12-r82. Epub 2003 Nov 25.


Microarray gene-expression profiles are generally validated one gene at a time by real-time RT-PCR. We describe here a different approach based on simultaneous mutual validation of large numbers of genes using two different expression-profiling platforms. The result described here for the NCI-60 cancer cell lines is a consensus set of genes that give similar profiles on spotted cDNA arrays and Affymetrix oligonucleotide chips. Global concordance is parameterized by a 'correlation of correlations' coefficient.

Publication types

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

MeSH terms

  • Algorithms
  • Cell Line, Tumor
  • Cluster Analysis
  • Gene Expression Profiling*
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Oligonucleotide Array Sequence Analysis / methods*