Tools and Strategies for Analyzing Toxicogenomics Data

These concerns were addressed, under FDA leadership, by a series of multicenter experiments by a consortium of academic, government, and commercial laboratories. 

Measurements of transcript abundance using the Affymetrix GeneChip platform is based upon probe sets consisting of eleven overlapping 25-mer oligonucleotide pairs arrayed on a silicon substrate. Each probe is arranged 

Raw gene expression data preprocessing produces tens of thousands of intensity values across multiple experiments. The most conunon strategy for analysis of this quantity of data usually begins with an analysis of differentially expressed up- or downregulated genes. This may be accomplished with 

TABLE 45.1 GeneChip Data Normalization and Summarization Algorithms 

RMA Quantile normalization—raw intensity values are preprocessed to create equally distributed data between chips accounts for experimentally observed patterns for probe behavior. Only uses perfect match (PM) probes in signal calculation Irizarry et al. (2003) 

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