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Genome Biology

, 6:P4 | Cite as

A novel scheme to assess factors involved in the reproducibility of DNA-microarray data

  • Sacha AFT van Hijum
  • Anne de Jong
  • Richard JS Baerends
  • Harma A Karsens
  • Naomi E Kramer
  • Rasmus Larsen
  • Chris D den Hengst
  • Casper J Albers
  • Jan Kok
  • Oscar P Kuipers
Deposited research article

Abstract

Background

In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective validation scheme was devised, implemented, and employed.

Results

A number of validation experiments were performed on Lactococcus lactis IL1403 amplicon-based DNA-microarrays. Using the validation scheme and ANOVA, the factors contributing to the variance in normalized DNA-microarray data were estimated. Day-to-day as well as experimenter-dependent variances were shown to contribute strongly to the variance, while dye and culturing had a relatively modest contribution to the variance.

Conclusions

Even in cases where 90 % of the data were kept for analysis and the experiments were performed under challenging conditions (e.g. on different days), the CV was at an acceptable 25 %. Clustering experiments showed that trends can be reliably detected also from (very) lowly expressed genes. The validation scheme thus allows determining conditions that could be improved to yield even higher DNA-microarray data quality.

Keywords

Lactis Validation Experiment Validation Scheme Additional Table Genome Biology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Copyright information

© BioMed Central Ltd 2005

Authors and Affiliations

  • Sacha AFT van Hijum
    • 1
  • Anne de Jong
    • 1
  • Richard JS Baerends
    • 1
  • Harma A Karsens
    • 1
  • Naomi E Kramer
    • 1
  • Rasmus Larsen
    • 1
  • Chris D den Hengst
    • 1
  • Casper J Albers
    • 2
  • Jan Kok
    • 1
  • Oscar P Kuipers
    • 1
  1. 1.Department of Molecular Genetics, University of GroningenGroningen Biomolecular Sciences and Biotechnology InstituteHarenthe Netherlands
  2. 2.Groningen Bioinformatics Centre, University of GroningenGroningen Biomolecular Sciences and Biotechnology InstituteHarenthe Netherlands

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