SCAN.UPC

The software tool "SCAN.UPC" addresses the challenge of integrating gene expression profiling data across different biotechnology platforms, which often produce data with platform-specific biases and unique raw-data distributions. This difficulty hampers efforts in data integration essential for consortia, researchers adopting new technologies, and those aggregating data from multiple experiments. SCAN.UPC introduces the Universal exPression Code (UPC) approach, which mitigates platform-specific noise by considering genomic base composition and target region length and employs a mixture model to determine gene activity in samples. It standardizes output values to a 0-to-1 scale, making data interpretation consistent across technologies and facilitating the development of technology-independent analysis pipelines. The UPC method is versatile and applicable to both one- and two-channel expression microarrays and RNA sequencing data without additional samples being needed during processing. This feature makes it particularly useful in personalized medicine, where individual sample processing is necessary.