Representation of Individual Gene Expression in Completely Pooled mRNA Samples

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  • GLASS Änne
    Institute for Medical Informatics and Biometry, University of Rostock, Medical Faculty
  • HENNING Jeannette
    Department of Neurology, Neurobiological Laboratory, University of Rostock, Medical Faculty
  • KAROPKA Thomas
    Institute for Medical Informatics and Biometry, University of Rostock, Medical Faculty
  • SCHEEL Thomas
    Institute for Medical Informatics and Biometry, University of Rostock, Medical Faculty
  • BANSEMER Sven
    Institute for Medical Informatics and Biometry, University of Rostock, Medical Faculty
  • KOCZAN Dirk
    Institute for Immunology, University of Rostock, Medical Faculty
  • GIERL Lothar
    Institute for Medical Informatics and Biometry, University of Rostock, Medical Faculty
  • ROLFS Arndt
    Department of Neurology, Neurobiological Laboratory, University of Rostock, Medical Faculty
  • GIMSA Ulrike
    Department of Neurology, Neurobiological Laboratory, University of Rostock, Medical Faculty

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Designing microarray experiments, scientists are often confronted with the question of pooling due to financial constraints, but discussion of the validity of pooling tends toward a sub-pooling recommendation. Since complete pooling protocols can be considered part of sub-pooling designs, gene expression data from three complete pooling experiments were analyzed. Data from complete pooled versus individual mRNA samples of rat brain tissue were compared to answer the question whether the pooled sample represents individual samples in small-sized experiments. Our analytic approach provided clear results concerning the Affymetrix® MAS 5.0 signal and detection call parameters. Despite a strong similarity of arrays within experimental groups, the individual signals were evidently not appropriately represented in the pooled sample, with slightly more than half of all the genes considered. Our analysis reveals problems in cases of small complete pooling designs with less than six subjects pooled.

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