Interface 2003

Exploration, Normalization, Summaries and Software of Affymetrix GeneChip Probe Level Data
Rafael Irizarry, (Johns Hopkins University),


High density oligonucleotide expression array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of oligonucleotides separately referred to as probes. Typically 12,000 to 20,000 probe sets are arrayed on a silicon chip. RNA samples are prepared, labeled and hybridized to the arrays. Arrays are then scanned, and images produced and analyzed to obtain an intensity value for each probe. These intensities quantify the extent of the hybridization between the labeled target sample and the oligonucleotide probe. A final step to obtain expression measures is to summarize the probe intensities for a given gene in order to quantify the amount of the corresponding mRNA species in the sample. Using two extensive spike-in studies and a dilution study, we performed a careful assessment of the method of summarizing probe level data provided by the current version of the Affymetrix Microarray Suite (MAS 5.0). Careful exploration of probe level data led us to expression measures derived from empirically motivated statistical models and appropriate normalization. The new expression measure greatly improves the performance of the Affymetrix technology. The advantages of a new expression measure are assessed through bias, variance, sensitivity, and specificity. We will also describe the software used for these analyses. A paper describing this example can be found on the web:

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