  One of the most popular tools for large scale gene expression studies are
high-density oligonucleotide (GeneChip(R)) arrays. These currently have 16-20
small probe cells (``features'') for evaluating the transcript abundance of
each gene. In addition, each probe is accompanied by a mismatched probe
designed as a control for non-specificity. An algorithm is presented to compute
comparative expression levels from the intensities of the individual features,
based on a statistical study of their distribution. Interestingly, MM probes
need not be included in the analysis. We show that our algorithm improves
significantly upon the current standard and leads to a substantially larger
number of genes brought above the noise floor for further analysis.
