Intensity-based analysis of two-colour microarrays enables efficient and flexible hybridization designs.

Peter A.C. 't Hoen, Rolf Turk, Judith M. Boer, Ellen Sterrenburg, Renée X. de Menezes, Gert Jan B. van Ommen, Johan T. den Dunnen

Onderzoeksoutput: Bijdrage aan tijdschriftArtikelpeer review

33 Citaten (Scopus)


In two-colour microarrays, the ratio of signal intensities of two co-hybridized samples is used as a relative measure of gene expression. Ratio-based analysis becomes complicated and inefficient in multi-class comparisons. We therefore investigated the validity of an intensity-based analysis procedure. To this end, two different cRNA targets were hybridized together, separately, with a common reference and in a self-self fashion on spotted 65mer oligonucleotide microarrays. We found that the signal intensity of the cRNA targets was not influenced by the presence of a target labelled in the opposite colour. This indicates that targets do not compete for binding sites on the array, which is essential for intensity-based analysis. It is demonstrated that, for good-quality arrays, the correlation of signal intensity measurements between the different hybridization designs is high (R > 0.9). Furthermore, ratio calculations from ratio- and intensity-based analyses correlated well (R > 0.8). Based on these results, we advocate the use of separate intensities rather than ratios in the analysis of two-colour long-oligonucleotide microarrays. Intensity-based analysis makes microarray experiments more efficient and more flexible: It allows for direct comparisons between all hybridized samples, while circumventing the need for a reference sample that occupies half of the hybridization capacity.

Originele taal-2Engels
Pagina's (van-tot)e41
TijdschriftNucleic Acids Research
Nummer van het tijdschrift4
StatusGepubliceerd - 2004
Extern gepubliceerdJa


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