Are data from different gene expression microarray platforms comparable?

Anna-Kaarina Järvinen, Sampsa Hautaniemi, Henrik Edgren, Petri Auvinen, Janna Saarela, Olli Kallioniemi, Outi Monni (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

165 Citations (Scopus)


Many commercial and custom-made microarray formats are routinely used for large-scale gene expression surveys. Here, we sought to determine the level of concordance between microarray platforms by analyzing breast cancer cell lines with in situ synthesized oligonucleotide arrays (Affymetrix HG-U95v2), commercial cDNA microarrays (Agilent Human 1 cDNA), and custom-made cDNA microarrays from a sequence-validated 13K cDNA library. Gene expression data from the commercial platforms showed good correlations across the experiments (r = 0.78–0.86), whereas the correlations between the custom-made and either of the two commercial platforms were lower (r = 0.62–0.76). Discrepant findings were due to clone errors on the custom-made microarrays, old annotations, or unknown causes. Even within platform, there can be several ways to analyze data that may influence the correlation between platforms. Our results indicate that combining data from different microarray platforms is not straightforward. Variability of the data represents a challenge for developing future diagnostic applications of microarrays.
Original languageEnglish
Pages (from-to)1164-1168
Issue number6
Publication statusPublished - 2004
MoE publication typeA1 Journal article-refereed


  • cDNA microarrays
  • Oligonucleotide microarrays
  • Quality control
  • Breast cancer


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