title: A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data.
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 genes with very low expression levels. The validation scheme thus allows determining conditions that could be improved to yield even higher DNA-microarray data quality.
authors.affiliation: Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands. s.a.f.t.van.hijum@rug.nl
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: van Hijum
authors.forename: Anne
authors.initials: A
authors.lastname: de Jong
authors.forename: Richard J S
authors.initials: RJ
authors.lastname: Baerends
authors.forename: Harma A
authors.initials: HA
authors.lastname: Karsens
authors.forename: Naomi E
authors.initials: NE
authors.lastname: Kramer
authors.forename: Rasmus
authors.initials: R
authors.lastname: Larsen
authors.forename: Chris D
authors.initials: CD
authors.lastname: den Hengst
authors.forename: Casper J
authors.initials: CJ
authors.lastname: Albers
authors.forename: Jan
authors.initials: J
authors.lastname: Kok
authors.forename: Oscar P
authors.initials: OP
authors.lastname: Kuipers
mesh_terms: D000704:Analysis of Variance; D001412:Bacillus subtilis / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D023281:Genomics / Q000379:methods*; D013294:Lactococcus lactis / Q000235:genetics; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011786:Quality Control; D015203:Reproducibility of Results; D012107:Research Design