Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells.
Lee JK,
Bussey KJ,
Gwadry FG,
Reinhold W,
Riddick G,
Pelletier SL,
Nishizuka S,
Szakacs G,
Annereau JP,
Shankavaram U,
Lababidi S,
Smith LH,
Gottesman MM,
Weinstein JN.
Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-8322, USA. jaeklee@virginia.edu
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.
PMID: 14659019 [PubMed - indexed for MEDLINE]
PMCID: PMC329421