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Nucleic Acids Research, 2003, Vol. 31, No. 23 e149
© 2003 Oxford University Press

Article

Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration

Chiara Romualdi, Silvia Trevisan, Barbara Celegato, Germano Costa1 and Gerolamo Lanfranchi*

CRIBI Biotechnology Centre and Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy and 1 Progetto Mantegna-Dipartimento di Fisica ‘Galileo Galilei’, Università degli Studi di Padova, Via F. Marzolo, 8, 35121 Padova, Italy

*To whom correspondence should be addressed. Tel: +39 049 8276221; Fax: +39 049 8276280; Email: lanfra{at}cribi.unipd.it

The variability of results in microarray technology is in part due to the fact that independent scans of a single hybridised microarray give spot images that are not quite the same. To solve this problem and turn it to our advantage, we introduced the approach of multiple scanning and of image integration of microarrays. To this end, we have developed specific software that creates a virtual image that statistically summarises a series of consecutive scans of a microarray. We provide evidence that the use of multiple imaging (i) enhances the detection of differentially expressed genes; (ii) increases the image homogeneity; and (iii) reveals false-positive results such as differentially expressed genes that are detected by a single scan but not confirmed by successive scanning replicates. The increase in the final number of differentially expressed genes detected in a microarray experiment with this approach is remarkable; 50% more for microarrays hybridised with targets labelled by reverse transcriptase, and 200% more for microarrays developed with the tyramide signal amplification (TSA) technique. The results have been confirmed by semi-quantitative RT–PCR tests.


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