Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments

In this paper we focus on the detection of differentially expressed genes a ccording to changes in hybridization signals using statistical tests. These tests were applied to 14 208 zebrafish cDNA clones that were immobilized o n a nylon support and hybridized with radioactively labeled target mRNA fro m wild-type and lithium-treated zebrafish embryos. The methods were evaluat ed with respect to 16 control clones that correspond to eight different gen es which are known to be involved in dorso-ventral axis specification. More over, 4608 Arabidopsis thaliana clones on the same array were used to judge statistical significance of expression changes and to control the false po sitive rates of the test decisions. Utilizing this special array design we show that differential expression of a high proportion of cDNA clones (15/1 6) and the respective genes (7/8) were identified, with a false positive er ror of <5% using the constant control data. Furthermore, we investigated th e influence of the number of repetitions of experiments on the accuracy of the procedures with experimental and simulated data. Our results suggest th at the detection of differential expression with repeated hybridization exp eriments is an accurate and sensitive way of identifying even small express ion changes (1:1.5) of a large number of genes in parallel.