PERSPECTIVES Two-Stage Testing in Microarray Analysis: What Is Gained?

standing changes in gene expression as a function of other observable or manipulable variables. However, microarrays also pose a number of new challenges. One of the most prominent of these is the difficulty in establishing a procedure for declaring whether a gene’s expression level is associated with the independent variable that offers reasonable and specifiable false-positive (type 1 error) and false-negative (type 2 error) rates. A recent article described a two-stage test-ing procedure to address these goals. However, information was not provided to indicate whether this procedure would or would not meet its objectives. Herein, we show mathematically that the two-stage procedure proposed does not provide benefits in terms of minimizing false-negatives while controlling the false-positive rate relative to standard single-stage testing. Therefore, investigators are encouraged to consider alternative analytic approaches. HE advent of microarray technology for gene expres-sion measurements opens many exciting opportunities and challenges in aging research (1,2). One of the major challenges involves determining whether a sample numeri-cal difference in gene expression among two or mor