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. CONCLUSION: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.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
van Hijum SA,de Jong A,Baerends RJ,Karsens HA,Kramer NE,Larsen R,den Hengst CD,Albers CJ,Kok J,Kuipers OPdoi
10.1186/1471-2164-6-77keywords:
subject
Has Abstractpub_date
2005-05-20 00:00:00pages
77issn
1471-2164pii
1471-2164-6-77journal_volume
6pub_type
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