Background: High-density oligonucleotide arrays have become a valuable tool for highthroughput gene expression profiling. Increasing the array information density and improving the analysis algorithms are two important computational research topics. Results: A new algorithm, Match-Only Integral Distribution (MOID), was developed to analyze high-density oligonucleotide arrays. Using known data from both spiking experiments and nochange experiments performed with Affymetrix GeneChip