Open Access

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

  • Sacha AFT van Hijum1,
  • Anne de Jong1,
  • Richard JS Baerends1,
  • Harma A Karsens1,
  • Naomi E Kramer1,
  • Rasmus Larsen1,
  • Chris D den Hengst1,
  • Casper J Albers2,
  • Jan Kok1 and
  • Oscar P Kuipers1Email author
Genome Biology20056:P4

DOI: 10.1186/gb-2005-6-4-p4

Received: 3 March 2005

Published: 3 March 2005

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.

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