This paper introduces a statistical methodology for the identification of differentially expressed genes in DNA microarray experiments based on multiple criteria. These criteria are false discovery rate (FDR), variance-normalized differential expression levels (paired t statistics), and minimum acceptable difference (MAD). The methodology also provides a set of simultaneous FDR confidence intervals on the true expression differences. The analysis can be implemented as a two-stage algorithm in which there is an initial screen that controls only FDR, which is then followed by a second screen which controls both FDR and MAD. It can also be implemented by computing and thresholding the set of FDR P values for each gene that satisfies the MAD criterion. We illustrate the procedure to identify differentially expressed genes from a wild type versus knockout comparison of microarray data.