Is it possible to quantify and rank the quality of several lists of significant genes found with gene expression profiling by different methods? High Performance Chip Data Analysis (HPCDA) improves expression profiling of Affymetrix chips via Bioretis database: you can easily use the default parameters and are sure to get the optimum of true positive results, independant of number of significant genes in your dataset. Gene List Significance Index (GLSI) quantifies quality of gene lists. With GLSI its easily judged which normalization/analyzing method gives better results. HPCDA score ranks by relevance.