Data management and analysis represent a major challenge for microarray studies. In this study, Affymetrix software was used to analyze an HIV-infection data. The microarray analysis shows remarkably different results when using different parameters provided by the software. This highlights the fact that a standardized analysis tool, incorporating biological information about the genes is needed in order to better interpret the microarray study. To address the data management problem, in-house programs, including scripts and a database, were designed. The in-house programs were also used to overcome problems and inconveniences discovered during the data analysis, including management of the gene lists. The database provides rapid connection to many online public databases, as well as the integration of the original microarray data, relevant publications and other useful information. The in-house programs allow investigators to process and analyze the full Affymetrix microarray data in a speedy manner.