Appendix A: Affymetrix U95A Experiment

This is a subset of Affymetrix data that was used to develop the MAS 5.0 algorithm, which generates gene expression intensities values from the 16 perfect match (PM) and mismatch (MM) probe pairs. This dataset was created by Affymetrix and is publicly available at their web site www.affymetrix.com; search on the phrase “Latin square data” to find the link to the page containing a description of the experiment and the downloadable files of data. Human cRNA fragments corresponding to 16 probesets on the HGU95A GeneChip were added to the hybridization mixture. Each array started with the same hybridization mixture from a common tissue source and the 16 probesets were spiked in concentrations ranging from 0 to 1024 pM. Specifically, the 16 cRNAs were spiked in according to 14 different concentrations (0, 0.25, 0.5, 1, 2, 4, . . . , 512, 1024 pM). Each concentration pattern of the 16 probesets were replicated three times with the exception of one pattern, which was only replicated twice; there were 59 arrays in this experiment. The cRNAs were spiked in at a different concentration on each array (apart from the replicates) arranged in a cyclic Latin square design. A more detailed description of this experiment is given by Irizarry et al. [2].