EzArray is an Affymetrix expression array data management and analysis system. EzArray can be used to manage and share data including projects, samples, raw array data files, and analysis results. EzArray includes three highly automated and seamlessly integrated data analysis programs named PreQ for data preprocessing and quality assessment, ProS for data processing and statistical testing, and RepA for report generating and gene annotation. Express Analysis is a one-step data analysis tool that covers all processing procedures in PreQ, ProS, and RepA. Microarray data can be from users' experiments (Custom Array Data), published raw array data (deposited CEL supplementary files in GEO), or GEO curated DataSets (GDS records). In addition, a number of standalone tools have been included in EzArray, including tools for gene annotation, array probe search, R shell for interactive execution of R scripts, and R batch for batch execution of R scripts.