Exploring Important Issues in The Implementation of Gene Set Enrichment Analysis
Yongjia Wang; Stanley J. Watson; Fan Meng
Advances in Bioinformatics and its Applications Series in Mathematical Biology and Medicine. 2005; 8:71-80.
Gene Set Enrichment Analysis (GSEA) was designed to detect subtle but coordinated differences in expression of a priori defined sets of functionally related genes . While GSEA can provide significant insights for the molecular mechanisms underlying many pathophysiological processes, there are concerns about its bias toward large gene sets. Computation time associated with some probe level analysis algorithms such as fitPLM  is also a major concern. We carried out systematic analyses on important issues related to GSEA and optimized the GSEA procedure for web implementation.