Different strategies may be used to draw conclusions from the data generated by DNA microarrays in our study of the effect of estradiol (E2) on the transcriptome of the mammary gland of mice. We selected two strategies: the first one involving a classification by cellular process of regulated genes, and the second one taking advantage of gene expression profile over a time course of treatment. We also used two standardization methods, MAS5.0 and RMA, in order to assess their similarities and differences leading us to a better understanding of their impact on the results. In comparing expression patterns of regulated genes by E2, we observed that there are good similarities between gene expression profiles obtained by MAS5.0 and RMA. However, when the ratio between signal intensities of treatment and control is low, differences between data normalized by MAS 5.0 and RMA are more apparent, i.e. where the discrimination between biological and technical variability is the least obvious.