Typically, how does one handle within-chip probe replicates on the Agilent microarray's to improve the significance of statistical tests? I am currently using limma, and probes seems to be treated individually and only replicates across chips are considered in the statistical tests. Tyler Reed Associate Bioinformatics Developer Thermo Scientific Genomics Thermo Fisher Scientific 2650 Crescent Drive, Suite 100 Lafayette, CO 80026 Direct: (303) 604-3265 tyler.reed@thermofisher.com<mailto:tyler.reed@thermofisher.com> www.thermoscientific.com/gen<http: www.thermoscientific.com="" gen=""> [[alternative HTML version deleted]]